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Supplementary Data

Supplementary Data

Supplemental Material

Materials and Methods

Immunohistochemistry

Primary antibodies used for validation studies include: mouse anti-desmoglein-3 (Cat. #

32-6300, Invitrogen, CA, USA; 1:25), rabbit anti- 4 (Cat. # ab11215, Abcam,

Cambridge, MA, USA; 1:100), mouse anti-cytokeratin 16 (Cat. # ab8741, Abcam; 1:25), rabbit

anti- antibody (Cat. # ab14418, Abcam; 1:200), mouse anti- (Cat. # M7020,

Dako, Carpinteria, CA, USA; 1:100). Secondary antibodies conjugated with (Vector,

Burlingame, CA, USA) were used, diluted to 1:400. Tissues slides containing archival FFPE

sections, or tissue micro arrays (TMA) consisting of 508 HNSCC and controls, were dewaxed in

SafeClear II (Fisher Scientific, Pittsburgh, PA, USA) hydrated through graded alcohols,

immersed in 3% hydrogen peroxide in PBS for 30 min to quench the endogenous peroxidase, and processed for antigen retrieval and immunostaining with the appropriate primary antibodies and

biotinylated secondary antibodies as described (1), followed by the avidin-biotin complex

method (Vector Stain Elite, ABC kit; Vector). Slides were washed and developed in 3,3'- diaminobenzidine (Sigma FASTDAB tablet; Sigma Chemical) under microscopic control, and counterstained with Mayer's hematoxylin. For each stained TMA the number of positive cells in each core was visually evaluated and the results expressed as a percentage of stained cells/ total number of cells. According to their immunoreactivity the tissues array cores were divided according to tumor differentiation, where the percentage of stained cells in the three tumor classes were scored as more than 5% and less than 25% of the cells stained, 26 to 50%, 51 to

75% or, 75 to 100%.

Patel et al., 1

Laser Capture Microdissection (LCM)

FFPE oral cancer tissue sections were deparaffinized in SafeClear II and hydrated

through graded alcohols to 70% ethanol. Slides were briefly washed in water and stained in

Mayer’s hematoxylin (10-15 sec) followed by dehydration through graded ethanol (70-100%)

and SafeClear II. For LCM, stained uncovered slides were air dried, and cells of interest captured

using a PIXCELL IIe (Molecular Devices Corporation, Sunnyvale, CA, USA) as described (2).

Approximately 20,000 cells were capture from a single or consecutive tissue sections using up to

4 CapSure LCM Caps (Molecular Devices Corporation), which were transferred to a 0.5 ml

sterile Eppendorf tube for extraction (see below).

Protein Extraction

Protein extraction was carried out using the Liquid Tissue MS Protein Prep kit according

to manufacturer’s protocol (Expression Pathology Inc., Gaithersburg, MD, USA). Briefly, the

films from the underside of the caps for each sample were removed, transferred to low binding reaction tubes, and incubated with 20 µl of Liquid Tissue extraction buffer at 950C for 1.5 h,

with intermittent mixing followed by a quickspin, to consolidate the material. Samples were

centrifuged at 10,000 rpm for 1 min, cooled on ice, followed by digestion with 1 µl of trypsin

(15-20 U/µl) for 1 h at 370C with intermittent mix and spin. The samples were centrifuged one

final time at 10,000 rpm for 1 min prior to reduction with 2 µl of 100 mM DTT (10 mM final

concentration) at 950C for 5 min, followed by centrifugation and storage at –80 0C until ready for analysis.

Patel et al., 2 Tandem Mass Spectrometry and Bioinformatic Analysis

FFPE extracted samples were acidified with 0.1% trifluoroacetic acid (TFA) and desalted

with C-18 ZipTip microcolumns (Millipore, Billerica, MA, USA), lyophilized to dryness,

resuspended in 0.1% TFA, and quantified by the BCA protein assay (Pierce, Rockford, IL,

USA). Nanoflow reversed-phase liquid chromatography (RPLC) was performed using an

Agilent 1100 capillary LC system (Agilent Technologies, Palo Alto, CA, USA) coupled online to a linear ion trap (LIT) mass spectrometer (LTQ, Thermo Electron, San Jose, CA, USA).

Separations were performed using 75 µm i.d. x 360 o.d. x 10 cm long fused silica capillary columns (Polymicro Technologies, Phoenix, AZ, USA) that were slurry packed in house with 3

µm, 300 Å pore size C-18 silica-bonded stationary phase (Vydac, Hysperia, CA, USA). After injecting 2 µL of sample (approximately 200 ng protein), the column was washed for 30 min with 98% mobile phase A (0.1% formic acid in water) at a flow rate of 0.5 µL/min. Peptides

were eluted using a linear gradient of 2% mobile phase B (0.1% formic acid in acetonitrile) to

40% solvent B in 110 minutes, then to 98% B in an additional 30 min, all at a constant flow rate

of 0.25 µL/min.

The LIT-MS was operated in a data dependent MS/MS mode in which each full MS scan

is followed by five MS/MS scans where the five most abundant peptide molecular ions are

selected for collision-induced dissociation (CID), using a normalized collision energy of 35%.

Dynamic exclusion was utilized to minimize redundant selection of peptides previously selected for CID. The heated capillary temperature and electrospray voltage were set at 160 ºC and 1.6 kV, respectively. Data were collected over a broad mass to charge (m/z) precursor ion selection scan range of 400-2000, followed by four segmented precursor selection scan ranges (e.g. gas

Patel et al., 3 phase fractionation in the m/z dimension, GPFm/z) using the following overlapping m/z intervals:

400-605, 595-805, 795-1205, and 1195-2000.

Tandem mass spectra were searched against the UniProt human protein database

(06/2005 release) from the European Bioinformatics Institute (http://www.ebi.ac.uk/integr8)

using SEQUEST (Thermo Electron). For a fully tryptic peptide to be considered legitimately

identified, it had to achieve stringent charge state and proteolytic cleavage-dependent cross

1+ 2+ 3+ correlation (Xcorr) scores of 1.9 for [M+H] , 2.2 for [M+2H] and 3.5 for [M+3H] , and a

minimum delta correlation ∆Cn) of 0.08. Results were further filtered using software developed

in-house to determine unique peptides and . Based on criteria followed in previous work,

the error in protein identification was <1.5% (3). To facilitate biological interpretation of the

protein lists derived from this experiment, data was subjected to EASE analysis (Expression

Analysis Systematic Explorer) to identify Ontology (GO) categories and terms that might indicate over-representation in the tissues analyzed.

References

1. Amornphimoltham P, Patel V, Sodhi A, et al. Mammalian target of rapamycin, a molecular target in squamous cell carcinomas of the head and neck. Cancer Res 2005;65:9953-61. 2. Baker H, Patel V, Molinolo AA, et al. Proteome-wide analysis of head and neck squamous cell carcinomas using laser-capture microdissection and tandem mass spectrometry. Oral Oncol 2005;41:183-99. 3. Hood BL, Darfler MM, Guiel TG, et al. Proteomic analysis of formalin-fixed prostate cancer tissue. Mol Cell Proteomics 2005;4:1741-53.

Patel et al., 4 Supplemental Table 1: Proteins identified in only in normal squamous epithelium

Peptides Accession Protein (number) Q12756 -like protein KIF1A (Axonal transporter of synaptic vesicles) 6 P35813 Protein phosphatase 2C alpha isoform (EC 3.1.3.16) (PP2C-alpha) (IA) (Protein phosphatase 1A) 3 Q9Y561 Low-density lipoprotein -related protein 12 precursor (Suppressor of tumorigenicity protein 7) 3 Q6ZN03 Hypothetical protein FLJ16545 3 O94916 Nuclear factor of activated T cells 5 (T cell NFAT5) (NF-AT5) (Tonicity-responsive 2 P23458 -protein kinase JAK1 (EC 2.7.1.112) (Janus kinase 1) (JAK-1) 2 P13611 Versican core protein precursor (Large fibroblast proteoglycan) (Chondroitin sulfate proteoglycan core 2 P16455 Methylated-DNA--protein- methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltra 2 Q9H0M3 Hypothetical protein DKFZp434O0710 (Hypothetical protein KIAA1549) 2 Q9UGU5 High-mobility group protein 2-like 1 (HMGBCG protein) 2 Q6ZWK7 Hypothetical protein FLJ16045 2 Q7Z7J3 Hypothetical protein 2 Q6UXX9 QFRL9384 2 Q96BY6 Dedicator of cytokinesis protein 10 (Protein zizimin 3) 2 O43693 -finger protein (Fragment) 1 P68106 FK506-binding protein 1B (EC 5.2.1.8) (Peptidyl-prolyl cis-trans 1B) (PPIase 1B) (Rotamase 1B) 1 P68402 Platelet-activating factor acetylhydrolase IB beta subunit (EC 3.1.1.47) (PAF acetylhydrolase 30 kDa sub 1 P78318 Immunoglobulin-binding protein 1 (CD79a-binding protein 1) (B cell signal transduction molecule alpha 4) 1 O15537 Retinoschisin precursor (X-linked juvenile retinoschisis protein) 1 P57082 T-box transcription factor TBX4 (T-box protein 4) 1 O43300 rich repeat neuronal protein 2 precursor (Leucine-rich repeat transmembrane neuronal 2 protein 1 P62906 60S ribosomal protein L10a (CSA-19) 1 P62690 HERV-K_22q11.23 provirus ancestral Gag polyprotein (Gag polyprotein) [Contains: Matrix protein; Capsid 1 P51813 Cytoplasmic tyrosine-protein kinase BMX (EC 2.7.1.112) (Bone marrow kinase BMX) (Epithelial and endoth 1 O60235 Airway trypsin-like protease precursor (EC 3.4.21.-) 1 P52961 GPI-linked NAD(P)(+)-- ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (Mono(ADP-ribosyl)tra 1 Q13445 Putative T1/ST2 receptor binding protein (Interleukin 1 receptor-like 1 ligand,) 1 P05937 Calbindin ( D-dependent calcium-binding protein, avian-type) (Calbindin D28) (D-28K) 1 Q14674 Separin (EC 3.4.22.49) (Separase) (Caspase-like protein ESPL1) (Extra spindle poles-like 1 protein) 1 Q13945 3',5'-cyclic AMP phosphodiesterase (Fragment) 1 Q13591 Semaphorin 5A precursor (Semaphorin F) (Sema F) 1 Q14202 protein 261 (DXS6673E protein) 1 P82650 Mitochondrial 28S ribosomal protein S22 (S22mt) (MRP-S22) (GK002) 1 O15234 Cancer susceptibility candidate gene 3 protein (Metastatic lymph node protein 51) (MLN 51 protein) (Bar 1 Q07001 Acetylcholine receptor protein, delta chain precursor 1 O15013 Rho guanine nucleotide exchange factor 10 1 O95602 DNA-directed RNA polymerase I largest subunit (EC 2.7.7.6) (RNA polymerase I 194 kDa subunit) (RPA1 1 P22455 Fibroblast growth factor receptor 4 precursor (EC 2.7.1.112) (FGFR-4) 1 P20711 Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC) 1 P23141 Liver carboxylesterase 1 precursor (EC 3.1.1.1) (Acyl :cholesterol acyltransferase) (ACAT) (M 1 P25054 Adenomatous polyposis coli protein (APC protein) 1 O95361 Tripartite motif protein 16 (Estrogen-responsive B box protein) 1 P13798 Acylamino-acid-releasing (EC 3.4.19.1) (AARE) (Acyl-peptide ) (APH) (Acylaminoacyl-pe 1 P12882 heavy chain, skeletal muscle, adult 1 (Myosin heavy chain IIx/d) (MyHC-IIx/d) 1 P11940 Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1) 1 P02649 Apolipoprotein E precursor (Apo-E) 1 P19878 Neutrophil factor 2 (NCF-2) (Neutrophil NADPH oxidase factor 2) (67 kDa neutrophil oxidase f 1 P00966 Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ) 1 P40394 Alcohol class IV mu/sigma chain (EC 1.1.1.1) (Retinol dehydrogenase) (Gastric alcohol dehy 1 O75206 Hypothetical protein A-152E5.9 1 P46100 Transcriptional regulator ATRX (X-linked II) (X-linked nuclear protein) (XNP) (Znf-HX) 1 P48167 receptor beta chain precursor (Glycine receptor 58 kDa subunit) 1 P48506 Glutamate--cysteine ligase catalytic subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamma- 1 O75128 KIAA0633 protein (Fragment) 1 P09529 Inhibin beta B chain precursor (Activin beta-B chain) 1 O75122 KIAA0627 protein (Fragment) 1 P43403 Tyrosine-protein kinase ZAP-70 (EC 2.7.1.112) (70 kDa zeta-associated protein) (Syk-related tyrosine ki 1 O75909 Cyclin K 1 P35080 -2 (Profilin II) 1 O75691 DRIM protein 1 Q9H1S9 DNA sequence from clone RP11-271B5 on 13 Contains the FGF9 fibroblast growth factor 9 1 Q9H0E7 Ubiquitin carboxyl-terminal hydrolase 44 (EC 3.1.2.15) (Ubiquitin thiolesterase 44) (Ubiquitin-specific pr 1 Q9BXG0 P231 1 Q9H4A3 /-protein kinase WNK1 (EC 2.7.1.37) (Protein kinase with no 1) (Protein kinase, lys 1 Q9BYM8 Ubiquitin conjugating enzyme 7 interacting protein 3 (Hepatitis B virus X-associated protein 4) (HBV ass 1 Q9H501 Hypothetical protein C20orf6 1 Q9H552 OTTHUMP00000021786 1 Q9H5T4 Hypothetical protein FLJ23059 1 Q96MQ1 Hypothetical protein FLJ32062 1 Q96NR3 Hypothetical protein FLJ30296 1 Q96HI0 Sentrin-specific protease 5 (EC 3.4.22.-) (Sentrin/SUMO-specific protease SENP5) (Protease FKSG45 1 Q96K08 Hypothetical protein FLJ14855 1 Q9BQ48 39S ribosomal protein L34, mitochondrial precursor (L34mt) (MRP-L34) 1 Q96RB7 Olfactory receptor 5M11 1 Q96RT8 Gamma- complex component 5 (GCP-5) 1 Q96RW7 Hemicentin 1 Q99704 Docking protein 1 (p62(dok)) (Downstream of tyrosine kinase 1) (pp62) 1 Q9UN73 Protocadherin alpha 6 precursor (PCDH-alpha6) 1 Q9UPA5 Bassoon protein (Zinc-finger protein 231) 1 Q9UQE7 Structural maintenance of chromosome 3 (Chondroitin sulfate proteoglycan 6) (Chromosome-associated 1 Q9UQP3 Tenascin N precursor 1 Q9UQR0 Sex comb on midleg-like protein 2 1 Q9UKR3 Kallikrein 13 precursor (EC 3.4.21.-) (Kallikrein-like protein 4) (KLK-L4) 1 Q9UKU9 Angiopoietin-related protein 2 precursor (Angiopoietin-like 2) (UNQ170/PRO196) 1 Q9UKV8 Eukaryotic translation initiation factor 2C 2 (eIF2C 2) (eIF-2C 2) 1 Q9UKX3 Myosin heavy chain, skeletal muscle, extraocular (MyHC-eo) 1 Q9UN33 Epstein-Barr virus-induced zinc finger protein (ZNF-EB) (CT-ZFP48) (Zinc finger protein dp) (ZNF-dp 1 Q9Y277 Voltage-dependent anion-selective channel protein 3 (VDAC-3) (hVDAC3) (Outer mitochondrial membran 1 Q9Y592 NY-REN-58 antigen 1 Q9Y2I0 KIAA0974 protein (Fragment) 1 Q9Y3T9 UPF0120 protein DKFZp564C186 1 Q9NXS3 BTB/POZ domain containing protein 5 1 Q9NVR7 Hypothetical protein FLJ10560 1 Q9NW08 DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide (EC 2.7.7.6) (RNA polymerase III sub 1 Q9NYU1 UDP-glucose:glycoprotein glucosyltransferase 2 precursor (EC 2.4.1.-) (UDP--Glc:glycoprotein glucosyltra 1 Q9NRA8 Eukaryotic translation initiation factor 4E transporter (eIF4E transporter) (4E-T) (Eukaryotic translati 1 Q9NTK5 Putative GTP-binding protein PTD004 (PRO2455) 1 Q9NV79 Protein C20orf36 1 Q9UBW7 Zinc finger protein 198 (Fused in myeloproliferative disorders protein) (Rearranged in atypical myelopro 1 Q9UBX1 Cathepsin F precursor (EC 3.4.22.41) (CATSF) 1 Q9UFE4 Hypothetical protein DKFZp434A128 1 Q9UID3 ANG2 ( open reading frame2) 1 Q9UH92 Transcription factor-like protein 4 (Max-like bHLHZip protein) (BigMax protein) (Mlx) 1 Q9P1Z3 Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 1 Q6ZU42 Hypothetical protein FLJ44010 1 Q6ZTQ0 Hypothetical protein FLJ44384 1 Q6ZW19 Hypothetical protein FLJ41761 1 Q6ZW52 Hypothetical protein FLJ41598 1 Q6ZTQ1 Hypothetical protein FLJ44382 1 Q6ZS91 Hypothetical protein FLJ45725 1 Q6ZSG2 Hypothetical protein FLJ45557 1 Q86UD0 Chromosome 9 open reading frame 140 (OTTHUMP00000064739) 1 Q86T65 Disheveled associated activator of morphogenesis 2 1 Q86UC4 RNA binding protein 1 Q86WW8 Hypothetical protein 1 Q7M4M4 Phosphorylation regulatory protein HP-10 1 Q7Z353 Hypothetical protein DKFZp686K21156 1 Q7Z4A1 MGC45780 1 Q6ZNE1 Hypothetical protein FLJ16186 1 Q5U5K5 CASC1 protein (Fragment) 1 Q5VTB9 Novel protein 1 Q5W0S6 Novel SPANX protein 1 Q15436 Protein transport protein Sec23A (SEC23-related protein A) 1 Q68DG2 Hypothetical protein DKFZp781J069 1 Q16164 G1 phase-specific gene protein (Fragment) 1 Q6P5U1 Hypothetical protein 1 Q6PN88 Hematopoietic stem/progenitor cell induced protein 2 (Fragment) 1 Q86XX4 Extracellular matrix protein FRAS1 precursor 1 Q6JEL2 Kelch-like protein 10 1 Q6P0M0 Hypothetical protein 1 Q8TEK3 -lysine N-methyltransferase, H3 lysine-79 specific (EC 2.1.1.43) (Histone H3-K79 methyltransfe 1 Q8TF01 SR rich protein 1 Q8WUA4 General transcription factor 3C polypeptide 2 (Transcription factor IIIC-beta subunit) (TF3C-beta) (TF 1 Q8WWF3 LOC136263 (Hypothetical protein FLJ40316) 1 Q8WWL2 Spir-2 protein (Fragment) 1 Q8NI84 OK/SW-CL.10 1 Q8TBY9 Hypothetical protein MGC33630 1 Q8TDD2 Transcription factor Sp7 (Zinc finger protein osterix) 1 Q8TDM0 Breast carcinoma amplified sequence 4 1 Q96C67 COL14A1 protein 1 Q92914 Fibroblast growth factor-11 (FGF-11) (Fibroblast growth factor homologous factor 3) (FHF-3) 1 Q8NGS5 Olfactory receptor 13C4 1 Q8N1N1 Hypothetical protein FLJ39107 1 Q8N338 Hypothetical protein (Fragment) 1 Q8IUA7 ATP-binding cassette sub-family A member 9 1 Q8IVF9 KIAA2012 protein (Fragment) 1 Q8NC19 Hypothetical protein FLJ90595 1 Q8NDC3 Hypothetical protein DKFZp547N1615 (Fragment) 1 Q8NDZ4 Hypothetical protein MGC33365 1 Q8NF91 Nesprin 1 (Nuclear envelope repeat protein 1) (Synaptic nuclear envelope protein 1) (Syne-1) (M 1 Q8N986 Hypothetical protein FLJ38225 1 Q8N7C3 Hypothetical protein FLJ25801 1 Q8N7S3 Hypothetical protein FLJ40411 1 Q8N8C9 Hypothetical protein FLJ39654 1 Q8N5D1 MRPL47 protein 1 Supplemental Table 2: Proteins identified only in well differentiated HNSCC

Peptides Accession Protein (number) Q13561 complex 50 kDa subunit (50 kDa -associated polypeptide) (p50 dynamitin) (DCT 5 Q9UKX2 Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain IIa) (MyHC-IIa) 4 P12883 Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta) 4 Q9BR76 Coronin-1B (Coronin-2) 3 P30049 ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14) 3 Q96E11 Mitochondrial ribosome recycling factor, isoform 1 3 P11216 Glycogen phosphorylase, brain form (EC 2.4.1.1) 3 Q08380 Galectin-3 binding protein precursor (Lectin galactoside-binding soluble 3 binding protein) (Ma 3 P11137 -associated protein 2 (MAP 2) (MAP-2) 3 P31025 Von Ebner's gland protein precursor (VEG protein) (Tear prealbumin) (TP) (Tear lipocalin) (Lipo 3 Q9HCF8 KIAA1614 protein (Fragment) 3 Q6NUR7 Villin 2 3 Q96PE1 Probable G protein-coupled receptor 124 precursor (Tumor endothelial marker 5) 2 P06732 kinase, M chain (EC 2.7.3.2) (M-CK) 2 Q96I25 Splicing factor 45 (45kDa splicing factor) (RNA binding motif protein 17) 2 P11678 Eosinophil peroxidase precursor (EC 1.11.1.7) (EPO) 2 Q9BVL4 Selenoprotein O 2 P12429 Annexin A3 (Annexin III) (Lipocortin III) (Placental anticoagulant protein III) (PAP-III) (35- 2 Q00587 CDC42 effector protein 1 (Serum protein MSE55) 2 Q14315 C (Gamma-filamin) (Filamin 2) (Protein FLNc) (-binding like protein) (ABP-L) (ABP- 2 P60866 40S ribosomal protein S20 2 Q9NS91 Postreplication repair protein RAD18 (hRAD18) (hHR18) (RING finger protein 73) 2 O15074 KIAA0368 protein (Fragment) 2 O60447 EVI-5 homolog 2 P04196 -rich glycoprotein precursor (Histidine- rich glycoprotein) (HPRG) 2 P58546 Myotrophin (V-1 protein) 2 P62805 Histone H4 2 P50416 Carnitine O-palmitoyltransferase I, mitochondrial liver isoform (EC 2.3.1.21) (CPT I) (CPTI-L) ( 2 P52292 Importin alpha-2 subunit (Karyopherin alpha-2 subunit) (SRP1-alpha) (RAG cohort protein 1) 2 P42261 Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (Glutamate receptor ionotropic, AM 2 P35998 26S protease regulatory subunit 7 (MSS1 protein) 2 Q9H7W7 Hypothetical protein FLJ14183 2 Q9Y6K5 2'-5'-oligoadenylate synthetase 3 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 3) (2-5A synthetase 2 Q9Y6L6 Solute carrier organic anion transporter family member 1B1 (Solute carrier family 21 member 2 Q9NQS5 Inflammation-related G protein-coupled receptor EX33 (Putative G-protein coupled receptor) 2 Q9NZH7 Interleukin 1 family member 8 (IL-1F8) (Interleukin-1 eta) (IL-1 eta) (FIL1 eta) (Interleukin-1 2 Q6ZNX0 Hypothetical protein FLJ26965 2 Q86W64 TPM1 protein (Fragment) 2 Q63HQ8 Hypothetical protein DKFZp686M21196 2 Q15485 Ficolin 2 precursor (Collagen/fibrinogen domain-containing protein 2) (Ficolin-B) (Ficolin B) (Se 2 Q15582 Transforming growth factor-beta induced protein IG-H3 precursor (Beta IG-H3) (Kerato-epit 2 Q8IYW7 Hypothetical protein (Fragment) 2 Q8IW93 Rho guanine nucleotide exchange factor (GEF) 19 (Novel protein) 2 Q8NE71 ATP-binding cassette, sub-family F, member 1 (ATP-binding cassette 50) (TNF-alpha stimulate 2 Q8N9S5 Hypothetical protein FLJ36608 2 Q96EP5 DAZ-associated protein 1 (Deleted in azoospermia-associated protein 1) 1 Q96F86 Hypothetical protein FLJ21128 (Hypothetical protein PP844) 1 Q8TDS5 G-protein coupled receptor TG1019 1 Q96I71 Zinc finger protein 42, isoform 1 1 Q96G74 Hypothetical protein DKFZp761A052 1 Q8WYH7 Hypothetical protein PP1009 1 Q96C19 EF-hand domain-containing protein 2 (Swiprosin 1) 1 Q96A55 Hypothetical protein MGC10485 1 P31415 Calsequestrin, skeletal muscle isoform precursor (Calsequestrin 1) (Calmitin) 1 Q9BS14 G2AN protein (Fragment) 1 Q9BTX7 Protein C20orf121 1 P08590 Myosin light polypeptide 3 ( 1, slow-twitch muscle B/ventricular isoform) (ML 1 P07602 Proactivator polypeptide precursor [Contains: Saposin A (Protein A); Saposin B (Sphingolipid ac 1 Q8TDG7 CLL-associated antigen KW-6 (Fragment) 1 Q96L12 Calreticulin 3 precursor (Calreticulin 2) 1 P20042 Eukaryotic translation initiation factor 2 subunit 2 (Eukaryotic translation initiation factor 2 b 1 Q96NJ6 Hypothetical protein FLJ30726 1 Q6ZQW7 Hypothetical protein FLJ46843 1 Q01650 Large neutral amino acids transporter small subunit 1 (L-type transporter 1) (4F2 lig 1 Q01831 DNA-repair protein complementing XP-C cells (Xeroderma pigmentosum group C complementing 1 Q6ZU46 Hypothetical protein FLJ44004 1 P36543 Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E s 1 Q6ZW16 Hypothetical protein FLJ41795 1 Q6ZUF0 Hypothetical protein FLJ43766 1 Q07325 Small inducible cytokine B9 precursor (CXCL9) (Gamma interferon induced monokine) (MIG) 1 Q6ZU30 Hypothetical protein FLJ44035 1 P84095 Rho-related GTP-binding protein RhoG 1 Q15738 NAD(P)-dependent dehydrogenase (EC 1.1.1.-) (H105e3 protein) 1 Q5U651 Ras-interacting protein 1 1 Q15466 0B2 (Orphan nuclear receptor SHP) (Small heterodimer partner) 1 Q15181 Inorganic pyrophosphatase (EC 3.6.1.1) (Pyrophosphate phospho-hydrolase) (PPase) 1 Q75VX8 KIAA2038 protein (Fragment) 1 Q6NVV8 LOC285148 protein (Fragment) 1 Q6N061 Hypothetical protein DKFZp686B2197 1 Q13402 Myosin VIIa 1 Q12972 Nuclear inhibitor of protein phosphatase-1 (NIPP-1) (Protein phosphatase 1, regulatory inhibito 1 Q69YW3 Hypothetical protein DKFZp434L2430 1 P42696 Probable RNA-binding protein KIAA0117 (HAL845) 1 Q8N9Y4 Hypothetical protein FLJ36068 1 Q8NBR8 Hypothetical protein FLJ90835 1 Q8N7Z5 Hypothetical protein FLJ40191 1 Q8N7J2 Hypothetical protein FLJ25477 1 P46721 Solute carrier organic anion transporter family member 1A2 (Solute carrier family 21 member 1 Q8TBG4 -glyoxylate aminotransferase 2-like 1 (Hypothetical protein FLJ34569) 1 P41236 Protein phosphatase inhibitor 2 (IPP-2) 1 Q8N3Y1 F-box/WD-repeat protein 8 (F-box and WD-40 domain protein 8) (F-box only protein 29) 1 P38159 Heterogeneous nuclear ribonucleoprotein G (hnRNP G) (RNA binding motif protein, X chromoso 1 Q8NCI1 Hypothetical protein FLJ90238 1 Q86VU5 Catechol-O-methyltransferase domain containing 1 (Methyltransferase) 1 Q86SQ9 Dehydrodolichyl diphosphate synthase (EC 2.5.1.-) (Dedol-PP synthase) 1 P59768 Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit (G gamma-I) 1 Q8IVG6 KIAA2004 protein (Fragment) 1 P62333 26S protease regulatory subunit S10B (Proteasome subunit p42) (Proteasome 26S subunit ATP 1 Q8N2K3 Hypothetical protein FLJ90162 1 O95239 Chromosome-associated kinesin KIF4A (Chromokinesin) 1 Q9HC99 P47ING3 protein (Hypothetical protein ING3) 1 Q9UDY2 Tight junction protein ZO-2 (Zonula occludens 2 protein) (Zona occludens 2 protein) (Tight jun 1 O75173 ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metalloproteinase with thrombospondi 1 O75163 KIAA0676 protein (Fragment) 1 P00973 2'-5'-oligoadenylate synthetase 1 (EC 2.7.7.-) ((2-5')oligo(A) synthetase 1) (2-5A synthetase 1 1 Q9HCK8 Chromodomain-helicase-DNA-binding protein 8 (CHD-8) (Helicase with SNF2 domain 1) (Fragm 1 P02585 C, skeletal muscle 1 Q9NR61 Delta-like protein 4 precursor (Drosophila Delta homolog 4) (UNQ1895/PRO4341) 1 Q9NVX2 WD-repeat protein HUSSY-07 1 Q9NRA0 Sphingosine kinase 2 (EC 2.7.1.-) (SK 2) (SPK 2) 1 O00548 Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1) (H-Delta-1) (UNQ146/PRO 1 Q9Y3E5 Peptidyl-tRNA hydrolase 2, mitochondrial precursor (EC 3.1.1.29) (PTH 2) (Bcl-2 inhibitor of tr 1 O15093 KIAA0393 protein (Fragment) 1 O15119 T-box transcription factor TBX3 (T-box protein 3) 1 Q9Y566 SH3 and multiple repeat domains protein 1 (Shank1) (Somatostatin receptor interactin 1 O00462 Beta-mannosidase precursor (EC 3.2.1.25) (Mannanase) (Mannase) 1 O00230 Cortistatin precursor [Contains: Cortistatin-29; Cortistatin-17] 1 Q9Y4H2 Insulin receptor -2 (IRS-2) 1 Q9ULX5 Zinc finger protein 179 (Brain finger protein) (RING finger protein 112) 1 Q9UHU3 PRO1659 1 Q9UKB5 Hypothetical protein MOT8 (Transmembrane protein SHREW1) 1 Q9UL15 BAG-family molecular chaperone regulator-5 (BAG-5) 1 Q9UHI8 ADAMTS-1 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin 1 O43405 Cochlin precursor (COCH-5B2) (UNQ257/PRO294) 1 O43168 KIAA0443 protein (Fragment) 1 Q9Y224 Protein C14orf166 (CGI-99) 1 O15143 ARP2/3 complex 41 kDa subunit (P41-ARC) (Actin-related protein 2/3 complex subunit 1B) 1 O60341 Amine oxidase flavin containing domain protein 2 (AOF2 protein) (BRAF-HDAC complex protein 1 Q9H8D6 Hypothetical protein FLJ13729 1 Q9H5W3 Hypothetical protein FLJ22944 1 Q9H816 Hypothetical protein FLJ13998 (DNA cross-link repair 1B) (PSO2 homolog, S. cerevisiae) (OTT 1 P04114 Apolipoprotein B-100 precursor (Apo B-100) [Contains: Apolipoprotein B-48 (Apo B-48)] 1 P06340 HLA class II histocompatibility antigen, DO alpha chain precursor (MHC class II antigen DOA 1 Q9HB48 Hypothetical protein 1 Q9H8K6 Hypothetical protein FLJ13491 1 P59533 Taste receptor type 2 member 38 (T2R38) (T2R61) (PTC bitter taste receptor) 1 P61289 Proteasome activator complex subunit 3 (Proteasome activator 28-gamma subunit) (PA28gamm 1 O43663 Protein regulating cytokinesis 1 (Protein regulator of cytokinesis 1, isoform 1) 1 P67809 Nuclease sensitive element binding protein 1 (Y box binding protein-1) (Y-box transcription fac 1 O43303 Centrosomal protein of 110 kDa (CP110 protein) 1 O43304 KIAA0420 protein (Fragment) 1 P62266 40S ribosomal protein S23 1 O60266 Adenylate cyclase type III (EC 4.6.1.1) (Adenylate cyclase, olfactive type) (ATP pyrophosphate 1 O60268 Protein KIAA0513 1 O60320 Hypothetical protein KIAA0574 (Fragment) 1 P51784 Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquitin thiolesterase 11) (Ubiquitin-sp 1 P09110 3-ketoacyl-CoA thiolase, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA 1 P50748 Kinetochore-associated protein 1 (Rough deal homolog) (hRod) (HsROD) (Rod) 1 P55145 ARMET protein precursor (Arginine-rich protein) 1 P54762 Ephrin type-B receptor 1 precursor (EC 2.7.1.112) (Tyrosine-protein kinase receptor EPH-2) (N 1 P55011 Solute carrier family 12 member 2 (Bumetanide-sensitive sodium-(potassium)-chloride cotrans 1 P55157 Microsomal triglyceride transfer protein large subunit precursor 1 O15287 Fanconi anemia group G protein (FACG protein) (DNA-repair protein XRCC9) 1 P55774 Small inducible cytokine A18 precursor (CCL18) (Macrophage inflammatory protein 4) (MIP-4) 1 P78333 Glypican-5 precursor 1 P57075 UBASH3A protein 1 O60237 Protein phosphatase 1 regulatory subunit 12B (Myosin phosphatase targeting subunit 2) (Myosi 1 Q13185 Chromobox protein homolog 3 (Heterochromatin protein 1 homolog gamma) (HP1 gamma) (Modif 1 Q13255 Metabotropic glutamate receptor 1 precursor (mGluR1) 1 Q13129 Zinc finger protein Rlf (Rearranged L- fusion gene protein) (Zn-15 related protein) 1 O00463 TNF receptor associated factor 5 (RING finger protein 84) 1 O14556 Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (EC 1.2.1.12) (Spermatogenic cell- 1 O00567 Nucleolar protein Nop56 (Nucleolar protein 5A) 1 Q13017 Rho-GTPase-activating protein 5 (p190-B) 1 Q13049 Tripartite motif protein 32 (EC 6.3.2.-) (Zinc-finger protein HT2A) (72 kDa Tat-interacting pr 1 Q14241 Transcription elongation factor B polypeptide 3 (RNA polymerase II transcription factor SIII 1 O00161 Synaptosomal-associated protein 23 (SNAP-23) (Vesicle-membrane fusion protein SNAP-23) 1 Q14721 Potassium voltage-gated channel subfamily B member 1 (Voltage-gated potassium channel subu 1 Q14766 Latent transforming growth factor beta binding protein, isoform 1L precursor (LTBP-1) (Trans 1 Q13618 Cullin homolog 3 (CUL-3) 1 P06454 Prothymosin alpha 1 P08069 Insulin-like growth factor I receptor precursor (EC 2.7.1.112) (CD221 antigen) 1 O15081 KIAA0376 protein (Fragment) 1 O15037 KIAA0323 protein (Fragment) 1 Q11206 CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta- 1 P78562 Phosphate regulating neutral endopeptidase (EC 3.4.24.-) (Metalloendopeptidase homolog PEX) 1 P08107 Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2) 1 Q00056 protein Hox-A4 (Hox-1D) (Hox-1.4) 1 O14791 Apolipoprotein L1 precursor (Apolipoprotein L-I) (Apolipoprotein L) (ApoL-I) (Apo-L) (ApoL) 1 P05455 Lupus La protein (Sjogren syndrome type B antigen) (SS-B) (La ribonucleoprotein) (La autoanti 1 O14879 Interferon-induced protein with tetratricopeptide repeats 3 (IFIT-3) (IFIT-4) (Interferon-i 1 Q08170 Splicing factor, arginine/serine-rich 4 (Pre-mRNA splicing factor SRP75) (SRP001LB) 1 Q08211 ATP-dependent RNA helicase A (Nuclear DNA helicase II) (NDH II) (DEAH-box protein 9) 1 P78344 Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 2) (eIF-4G 2) (eIF4G 2) (p97 1 Q02252 Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27 1 Q06418 Tyrosine-protein kinase receptor TYRO3 precursor (EC 2.7.1.112) (Tyrosine-protein kinase RSE 1 P23229 Integrin alpha-6 precursor (VLA-6) (CD49f) 1 Q6MZR4 Hypothetical protein DKFZp779N1969 (Fragment) 1 O95684 FGFR1 oncogene partner (FOP) (OTTHUMP00000017612) (Fragment) 1 O95503 Chromobox protein homolog 6 1 P20592 Interferon-regulated resistance GTP-binding protein MxB (p78-related protein) 1 O95398 RAP guanine-nucleotide-exchange factor 3 (cAMP-regulated guanine nucleotide exchange facto 1 P20849 Collagen alpha 1(IX) chain precursor 1 O95764 Hypothetical protein WUGSC:H_DJ0901A04.1 (Fragment) 1 P24539 ATP synthase B chain, mitochondrial precursor (EC 3.6.3.14) 1 O95235 Kinesin family member 20A (Rabkinesin-6) (Rab6-interacting kinesin-like protein) (GG10_2) 1 P04150 (GR) 1 P23468 Receptor-type tyrosine-protein phosphatase delta precursor (EC 3.1.3.48) (Protein-tyrosine ph 1 P24046 Gamma-aminobutyric-acid receptor rho-1 subunit precursor (GABA(A) receptor) 1 P11177 E1 component beta subunit, mitochondrial precursor (EC 1.2.4.1) (PDH 1 P01042 Kininogen precursor (Alpha-2-thiol proteinase inhibitor) [Contains: Bradykinin (Kallidin I); Lysy 1 P02730 Band 3 anion transport protein (Anion exchange protein 1) (AE 1) (CD233 antigen) 1 P11487 INT-2 proto-oncogene protein precursor (Fibroblast growth factor-3) (FGF-3) (HBGF-3) 1 P15144 Aminopeptidase N (EC 3.4.11.2) (hAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (A 1 P18859 ATP synthase coupling factor 6, mitochondrial precursor (EC 3.6.3.14) (F6) 1 P16152 Carbonyl reductase [NADPH] 1 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 1) (Prosta 1 P41212 Transcription factor ETV6 (ETS-related protein Tel1) (Tel) (ETS translocation variant 6) 1 P09923 Alkaline phosphatase, intestinal precursor (EC 3.1.3.1) (IAP) 1 P09914 Interferon-induced protein with tetratricopeptide repeats 1 (IFIT-1) (Interferon-induced 56 1 P36405 ADP-ribosylation factor-like protein 3 1 O75223 Protein C7orf24 1 P42694 Potential helicase with zinc-finger domain 1 P10619 Lysosomal protective protein precursor (EC 3.4.16.5) (Cathepsin A) (Carboxypeptidase C) (Prot 1 O60884 DnaJ homolog subfamily A member 2 (HIRA interacting protein 4) (Cell cycle progression rest 1 P48426 Phosphatidylinositol-4-phosphate 5-kinase type II alpha (EC 2.7.1.149) (PIP5KII-alpha) (1-phos 1 P42695 Hypothetical protein KIAA0056 (Fragment) 1 O75055 KIAA0467 protein (Fragment) 1 P43307 Translocon-associated protein, alpha subunit precursor (TRAP-alpha) (Signal sequence recepto 1 P30533 Alpha-2-macroglobulin receptor-associated protein precursor (Alpha-2-MRAP) (Low density lip 1 O94822 Zinc finger protein 294 1 P28340 DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA polymerase delta subunit p125) 1 P28907 ADP-ribosyl cyclase 1 (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 1) (cADPr hydrolase 1) (Lympho 1 P34932 Heat shock 70 kDa protein 4 (Heat shock 70-related protein APG-2) (HSP70RY) 1 P35275 Zinc finger protein 126 (HZF-2) (Fragment) 1 P35609 Alpha- 2 (Alpha actinin skeletal muscle isoform 2) (F-actin cross linking protein) 1 O75762 Transient receptor potential cation channel subfamily A member 1 (Ankyrin-like with transmem 1 O75665 Oral-facial-digital syndrome 1 protein (Protein 71-7A) 1 Q9GZN6 Orphan sodium- and chloride-dependent neurotransmitter transporter NTT5 (Solute carrier f 1 Q9GZU8 NEFA-interacting nuclear protein NIP30 (CDA10/CDA018) 1 Q9GZZ9 Hypothetical protein DKFZp434C2415 (Ubiquitin-activating enzyme E1-domain containing 1, iso 1 Q9H1I8 Activating signal cointegrator 1 complex subunit 2 (ASC-1 complex subunit p100) (Trip4 comple 1 Q9C0E2 Exportin 4 (Exp4) 1 Q9H251 -23 precursor (Otocadherin) 1 Q9H2T7 Ran-binding protein 17 1 Q9BYT9 Transmembrane protein 16C 1 Q9BYW2 Huntingtin interacting protein 1 1 Q9BYZ6 Rho-related BTB domain-containing protein 2 (Deleted in breast cancer 2 gene protein) (p83) 1 Q9C060 LYST-interacting protein LIP8 (Fragment) 1 Q9H3P7 Golgi resident protein GCP60 (Acyl-Coenzyme A binding domain containing 3) (Golgi phosphopro 1 Q9H974 Hypothetical protein FLJ12960 (QTRTD1 protein) (Queuine tRNA-ribosyltransferase domain c 1 Q9H9U2 Hypothetical protein FLJ12548 1 Q9HAA5 Hypothetical protein FLJ11889 1 Q9NNW5 WD-repeat protein 6 1 Q9NP55 Protein Plunc precursor (Palate lung and nasal epithelium clone protein) (Lung specific X protein 1 Q96EY1 DnaJ homolog subfamily A member 3, mitochondrial precursor (Tumorous imaginal discs protei 1 Q9H8U9 Hypothetical protein FLJ13213 1 Q9H788 Hypothetical protein FLJ21146 1 Q9H7Z3 Protein C14orf102 1 Q9H819 Hypothetical protein FLJ13992 (Hypothetical protein MGC29463) 1 Q9H5W0 Hypothetical protein FLJ22961 1 Q96NL8 Hypothetical protein FLJ30600 1 Q9BUF5 Tubulin beta MGC4083 1 Q96MT8 Centrosomal protein of 63 kDa (Cep63 protein) 1 Q96QE3 ATP(GTP)-binding protein 1 Q96QH7 DJ54B20.4 (Novel KRAB box containing C2H2 type zinc finger protein) 1 Q96N64 Hypothetical protein FLJ31359 1 Q6KC79 Nipped-B-like protein (Delangin) (SCC2 homolog) 1 Q96G01 -like bicaudal D protein homolog 1 1 Q96HE7 ERO1-like protein alpha precursor (EC 1.8.4.-) (ERO1-Lalpha) (Oxidoreductin 1-lalpha) (Endopla 1 Q96HR9 open reading frame 32 1 Q96K12 Hypothetical protein FLJ14850 (Male sterility domain containing 1) 1 Q96KJ4 Similar to pre-pro-megakarycyte potentiating factor 1 Q99856 AT-rich interactive domain-containing protein 3A (ARID domain-containing protein 3A) (B-cell 1 Q96RY5 Hypothetical protein KIAA1426 1 Q99457 Nucleosome assembly protein 1-like 3 1 Q99467 CD180 antigen precursor (Lymphocyte antigen 64) (Radioprotective 105 kDa protein) 1 Q99572 P2X purinoceptor 7 (ATP receptor) (P2X7) (Purinergic receptor) (P2Z receptor) 1 Q9UP23 PhLP1 1 Q9UPT8 KIAA1064 protein (Fragment) 1 Q9UPU3 VPS10 domain-containing receptor SorCS3 precursor 1 Q9UPX3 KIAA1027 protein (Fragment) 1 Q9UQL6 5 (HD5) (Antigen NY-CO-9) 1 Q9UPV7 KIAA1045 protein (Fragment) 1 Q9UKV3 Apoptotic chromatin condensation inducer in the nucleus (Acinus) 1 Q9ULH6 BIG3 1 Q9ULJ8 Neurabin-I (Neural tissue-specific F-actin binding protein I) (Protein phosphatase 1 regulatory 1 Q9ULV8 Signal transduction protein CBL-C (SH3-binding protein CBL-C) (CBL-3) (RING finger protein 5 1 Q9UKY1 Zinc fingers and protein 1 1 Q9Y4L2 Zinc finger protein PLAG1 1 Q9Y4Z2 Neurogenin 3 1 Q9Y6B5 PAK2 1 Q9Y5Q9 General transcription factor 3C polypeptide 3 (Transcription factor IIIC-gamma subunit) (TF3 1 Q9Y2D9 KIAA0924 protein (Fragment) 1 Q9Y2V6 Hypothetical protein (Cardiac ankyrin repeat kinase) (OTTHUMP00000058703) 1 Q9Y4I0 Zinc-finger helicase 1 Q9Y3E1 CGI-142 protein (Hepatoma-derived growth factor 2) (Hypothetical protein FLJ10418) (Hepat 1 Q9Y4E5 Zinc finger protein 451 (Coactivator for steroid receptors) 1 Q9UJV9 DEAD-box protein abstrakt homolog (DEAD-box protein 41) 1 Q9NW14 Hypothetical protein FLJ10376 1 Q9NW75 G patch domain containing protein 2 1 Q9NWU1 Hypothetical protein FLJ20604 1 Q9NVE7 Pantothenate kinase 4 (EC 2.7.1.33) (Pantothenic acid kinase 4) (hPanK4) 1 Q9NY33 Dipeptidyl-peptidase III (EC 3.4.14.4) (DPP III) (Dipeptidyl aminopeptidase III) (Dipeptidyl a 1 Q9NYU2 UDP-glucose:glycoprotein glucosyltransferase 1 precursor 1 Q9NYY3 Serine/threonine-protein kinase PLK2 (EC 2.7.1.37) (Polo-like kinase 1) (PLK-2) (Serine/threon 1 Q9NRY4 Glucocorticoid receptor DNA binding factor 1 (Glucocorticoid receptor repression factor 1) (G 1 Q9NR96 Toll-like receptor 9 precursor 1 Q9NR99 Adlican 1 Q9NVN3 Hypothetical protein FLJ10620 1 Q9NZ71 Regulator of telomere elongation helicase 1 (Helicase-like protein NHL) 1 Q9NS28 Regulator of G-protein signaling 18 (RGS18) 1 Q9NRC8 NAD-dependent deacetylase 7 (EC 3.5.1.-) (SIR2-like protein 7) 1 Q9UHG0 Doublecortin domain-containing protein 2 (RU2S protein) 1 Q9NZ08 Adipocyte-derived leucine aminopeptidase precursor (EC 3.4.11.-) (A-LAP) (ARTS-1) (Aminopep 1 Q9UBF2 Coatomer gamma-2 subunit (Gamma-2 coat protein) (Gamma-2 COP) 1 Q9UHV7 Thyroid -associated 240 kDa component (Trap240) (Activat 1 Q9UI12 Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump H 1 Q9P246 Stromal interaction molecule 2 precursor 1 Q9NZJ4 Sacsin 1 Q9UBR4 LIM/homeobox protein Lhx3 1 Q9P2N4 ADAMTS-9 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin 1 Q9UBB4 Ataxin-10 (Spinocerebellar ataxia type 10 protein) (Brain protein E46 homolog) 1 Q6ZVI2 Hypothetical protein FLJ42553 1 Q71RB0 PP7302 1 Q6ZU14 Hypothetical protein FLJ44063 1 Q6ZNJ8 FLJ00321 protein (Fragment) 1 Q6ZNZ8 Hypothetical protein FLJ26816 1 Q6ZP70 Hypothetical protein FLJ26432 1 Q6ZP82 Hypothetical protein FLJ26337 1 Q6ZR15 Hypothetical protein FLJ46734 1 Q6ZR28 Hypothetical protein FLJ46703 1 Q6ZR96 Hypothetical protein FLJ46536 1 Q71RB1 PP7080 1 Q6ZRR7 Hypothetical protein FLJ46156 1 Q6ZT48 Hypothetical protein FLJ44959 1 Q86T31 Hypothetical protein DKFZp313K2238 1 Q86TV4 Full-length cDNA clone CS0DI085YI08 of Placenta of Homo sapiens (human) (Fragment) 1 Q86UE4 LYRIC protein (Lysine-rich CEACAM1 co-isolated protein) (3D3/lyric) (Metastasis adhesion pr 1 Q7RTR4 NOD16 1 Q7RTU8 Harmonin isoform b3 1 Q7Z2R7 MSTP131 1 Q7Z524 HUMEEP 1 Q7Z5L9 Interferon regulatory factor-2 binding protein 2A 1 Q7Z6J8 C6orf157 protein (Fragment) 1 Q7Z6L5 MYO1B protein 1 Q16799 Reticulon 1 (Neuroendocrine-specific protein) 1 Q16650 T-brain-1 protein (T-box brain protein 1) (TBR-1) (TES-56) 1 Q5W064 Lipase-like, ab-hydrolase domain containing 1 1 Q15006 Tetratricopeptide repeat protein KIAA0103 1 Q15051 IQ calmodulin-binding motif containing protein 1 1 Q15417 Calponin-3 (Calponin, acidic isoform) 1 Q15751 P532 1 Q15927 DNA-binding protein (Fragment) 1 Q6PH81 Similar to RIKEN cDNA 4921524J17 1 Q6UB98 Ankyrin repeat domain protein 12 (Ankyrin repeat-containing -2) (GAC-1 protein) 1 Q6URC4 Diaphanous 1 1 Q6UWF8 VSSW1971 1 Q6UWT9 APRG372 1 Q6NE83 Hypothetical protein DKFZp686O06111 1 Q68D79 Hypothetical protein DKFZp686K16211 1 Q8TEF8 FLJ00239 protein (Fragment) 1 Q8TEW8 Amyotrophic lateral sclerosis 2 chromosome region candidate gene protein 19 (Partitioning-def 1 Q8WTW4 Tumor suppressor candidate 4 (NPR2-like) (Gene 21 protein) (G21 protein) 1 Q8WVS4 Hypothetical protein FLJ10300 1 Q8WVU3 HT007 protein 1 Q86XD5 KIAA0773 protein 1 Q8NHS5 RNF151 protein (Fragment) 1 Q8TAV4 Stomatin-like 3 1 Q8TB36 Ganglioside-induced differentiation-associated protein 1 (GDAP1) 1 Q8TBX8 Phosphatidylinositol-4-phosphate 5-kinase, type II, gamma 1 Q8TCU5 Glutamate [NMDA] receptor subunit 3A precursor (N-methyl-D-aspartate receptor subtype N 1 Q8TDX9 Polycystic kidney disease 1-like 1 protein (Polycystin 1L1) 1 Q969J3 LOH12CR1 (Hypothetical protein FLJ90547) (LOH1CR12) 1 Q96AJ9 Vesicle transport through interaction with t-SNAREs homolog 1A (Vesicle transport v-SNARE 1 Q93038 Tumor necrosis factor receptor superfamily member 25 precursor (WSL-1 protein) (Apoptosis 1 Q92993 Histone acetyltransferase HTATIP (EC 2.3.1.48) (60 kDa Tat interactive protein) (Tip60) (HIV 1 Q96CX6 Hypothetical protein (Fragment) 1 Q96BD8 open reading frame 24 1 Q8WYS0 GL013 1 Q8WYZ7 Hypothetical protein 1 Q8WZA2 RAP guanine-nucleotide-exchange factor 4 (cAMP-regulated guanine nucleotide exchange facto 1 Q92538 Golgi-specific brefeldin A-resistance guanine nucleotide exchange factor 1 (BFA-resistant GEF 1 Q92618 Zinc finger protein 516 1 Q92625 Ankyrin repeat and SAM domain protein 1 1 Q92764 , type I cuticular HA5 (, type I HA5) 1 Q92966 snRNA activating protein complex 50 kDa subunit (SNAPc 50 kDa subunit) (Proximal sequence 1 Q8IZA3 Oocyte-specific histone H1 1 Q8N2E9 Hypothetical protein PSEC0211 1 Q8N4U5 Hypothetical protein MGC40368 1 Q8N1Q8 Hypothetical protein FLJ37964 1 Q8IVE6 KIAA2025 protein (Fragment) 1 Q8IWN7 Retinitis pigmentosa 1-like 1 protein 1 Q8IXT5 Similar to RIKEN cDNA 3000004N20 1 Q8NDZ6 Hypothetical protein MGC33214 1 Q8ND90 Paraneoplastic antigen Ma1 (Neuron- and testis-specific protein 1) (37 kDa neuronal protein) 1 Q8NE67 NYD-SP12 protein 1 Q8NF24 FLJ00378 protein (Fragment) 1 Q8NF50 Dedicator of cytokinesis protein 8 (Fragment) 1 Q8NF99 Zinc finger protein 397 (Zinc finger and SCAN domain containing protein 15) 1 Q14827 MG21 protein (Fragment) 1 Q8NDW3 Zinc finger protein 33b (Zinc finger protein 11b) (KOX 2) 1 Q8N6F8 Williams-Beuren syndrome chromosome region 27 (WBSCR27) (Williams-Beuren syndrome crit 1 Q8N8D6 Hypothetical protein FLJ39636 1 Q8NBU9 Hypothetical protein FLJ90734 (PP10933) 1 Q8N991 Hypothetical protein FLJ38192 1 Q8N9V7 Hypothetical protein FLJ36157 1 Supplemental Table 3: Proteins identified only in mild differentiated HNSCC

Peptides Accession Protein (number) Q9Y3Z3 SAM domain and HD domain-containing protein 1 (Dendritic cell-derived IFNG-induced protein) 5 P50914 60S ribosomal protein L14 (CAG-ISL 7) 3 Q13057 Bifunctional coenzyme A synthase (CoA synthase) (NBP) (POV-2) [Includes: Phosphopantethein 3 P45974 Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin thiolesterase 5) (Ubiquitin-spec 3 P49588 Alanyl-tRNA synthetase (EC 6.1.1.7) (Alanine--tRNA ligase) (AlaRS) 2 Q12996 Cleavage stimulation factor 77kDa subunit 2 Q14624 Inter-alpha-trypsin inhibitor heavy chain H4 precursor (ITI heavy chain H4) (Inter-alpha-inhib 2 O15032 KIAA0316 protein (Fragment) 2 Q01955 Collagen alpha 3(IV) chain precursor (Goodpasture antigen) 2 O95661 Rho-related GTP-binding protein RhoI 2 P23921 Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleoside-diphosphate r 2 P02656 Apolipoprotein C-III precursor (Apo-CIII) (ApoC-III) 2 P12018 Immunoglobulin iota chain precursor (V(pre)B protein) (VpreB protein) (CD179a antigen) 2 O75348 Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump 2 P38606 Vacuolar ATP synthase catalytic subunit A, ubiquitous isoform (EC 3.6.3.14) (V-ATPase A subun 2 Q9HBK9 Cyt19 2 Q96KR5 Leishmanolysin-like peptidase, variant 2 (EC 3.4.24.36) 2 Q9BU70 Chromosome 9 open reading frame 156 2 Q9Y265 RuvB-like 1 (EC 3.6.1.-) (49-kDa TATA box-binding protein-interacting protein) (49 kDa TBP-int 2 Q9ULV0 Myosin Vb (Myosin 5B) 2 Q9NWL6 Hypothetical protein FLJ20752 (HCV NS3-transactivated protein 1) 2 Q9UJ70 N-acetylglucosamine kinase (EC 2.7.1.59) (GlcNAc kinase) 2 Q6ZRD7 Hypothetical protein FLJ46433 2 Q7Z7A1 CENTRIOLIN 2 Q8TE28 BA351K23.4 (Novel protein) (Hypothetical protein FLJ25831) 2 Q8IYW2 Chromosome 10 open reading frame 92 2 Q8N7E2 Hypothetical protein FLJ25735 2 P59045 NACHT-, LRR- and PYD-containing protein 11 (PYRIN-containing APAF1-like protein 6) (Nucleot 1 P62191 26S protease regulatory subunit 4 (P26s4) (Proteasome 26S subunit ATPase 1) 1 O43432 Eukaryotic translation initiation factor 4 gamma 3 (eIF-4-gamma 3) (eIF-4G 3) (eIF4G 3) (eIF 1 P58107 Epiplakin (450 kDa epidermal antigen) 1 O43681 Arsenical pump-driving ATPase (EC 3.6.3.16) (Arsenite-translocating ATPase) (Arsenical resista 1 O43583 Density-regulated protein (DRP) (DRP1 protein) (Smooth muscle cell associated protein-3) (SM 1 O43156 Protein KIAA0406 1 O15398 N-methyl-D-aspartate receptor 2C subunit precursor 1 O15372 Eukaryotic translation initiation factor 3 subunit 3 (eIF-3 gamma) (eIF3 p40 subunit) (eIF3h) 1 O43182 Rho-GTPase-activating protein 6 (Rho-type GTPase-activating protein RhoGAPX-1) 1 O60275 KIAA0522 protein (Fragment) 1 P51572 B-cell receptor-associated protein 31 (BCR-associated protein Bap31) (p28 Bap31) (CDM protei 1 P49646 Very very hypothetical protein RMSA-1 1 P48681 1 P49247 Ribose-5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase) 1 P09001 Mitochondrial 39S ribosomal protein L3 (L3mt) (MRP-L3) 1 P50443 Sulfate transporter (Diastrophic dysplasia protein) 1 O43836 NMDA receptor glutamate-binding chain (Fragment) 1 P52701 DNA mismatch repair protein MSH6 (MutS-alpha 160 kDa subunit) (G/T mismatch binding prot 1 P05161 Ubiquitin cross-reactive protein precursor (Interferon-induced 17 kDa protein) (Interferon-in 1 O60229 Huntingtin-associated protein-interacting protein (Duo protein) 1 P54132 Bloom's syndrome protein (EC 3.6.1.-) (RecQ protein-like 3) (DNA helicase, RecQ-like, type 2) 1 P52789 Hexokinase, type II (EC 2.7.1.1) (HK II) (Muscle form hexokinase) 1 P53675 Clathrin heavy chain 2 (CLH-22) 1 P53992 Protein transport protein Sec24C (SEC24-related protein C) 1 P51888 Prolargin precursor (Proline-arginine-rich end leucine-rich repeat protein) 1 P52566 Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (Ly-GDI) 1 O00571 DEAD-box protein 3 (Helicase-like protein 2) (HLP2) (DEAD-box, X isoform) 1 O00515 Ladinin 1 (Lad-1) (120 kDa linear IgA bullous dermatosis antigen) (97 kDa linear IgA bullous der 1 Q13427 Peptidyl-prolyl cis-trans isomerase G (EC 5.2.1.8) (Peptidyl-prolyl isomerase G) (PPIase G) (Rota 1 Q13283 Ras-GTPase-activating protein binding protein 1 (GAP SH3-domain binding protein 1) (G3BP-1) ( 1 Q12887 Protoheme IX farnesyltransferase, mitochondrial precursor (EC 2.5.1.-) ( O synthase) 1 Q13023 A-kinase anchor protein 6 (Protein kinase A anchoring protein 6) (PRKA6) (A-kinase anchor prot 1 Q13459 Myosin IXb (Unconventional myosin-9b) 1 P06744 Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohe 1 Q13698 Voltage-dependent L-type calcium channel alpha-1S subunit (Voltage-gated calcium channel alph 1 Q14088 Ras-related protein Rab-33A (Small GTP-binding protein S10) 1 O00311 Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7-related kinase) (HsCdc7) (huCdc7 1 Q14151 Scaffold attachment factor B2 1 Q01130 Splicing factor, arginine/serine-rich 2 (Splicing factor SC35) (SC-35) (Splicing component, 35 1 Q01970 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3 (EC 3.1.4.11) (Phosphoinositid 1 O15263 Beta-defensin 2 precursor (BD-2) (hBD-2) (Defensin, beta 2) (Skin-antimicrobial peptide 1) (SA 1 Q00013 55 kDa erythrocyte membrane protein (p55) (Membrane protein, palmitoylated 1) 1 Q08257 Quinone (EC 1.6.5.5) (NADPH:quinone reductase) (Zeta-crystallin) 1 O14776 Transcription elongation regulator 1 (TATA box-binding protein-associated factor 2S) (Transc 1 O14771 Zinc finger protein 213 (Putative transcription factor CR53) 1 P07711 Cathepsin L precursor (EC 3.4.22.15) (Major excreted protein) (MEP) 1 O14810 Complexin 1 (Synaphin 2) 1 O15020 Spectrin beta chain, brain 2 (Spectrin, non-erythroid beta chain 2) (Beta-III spectrin) 1 Q02818 Nucleobindin 1 precursor (CALNUC) 1 O14907 Tax interaction protein 1 (-interacting protein 3) (Tax-interacting protein 1) (Tax1 1 Q06250 Wilms' tumor associated protein (WIT-1) 1 P21817 Ryanodine receptor 1 (Skeletal muscle-type ryanodine receptor) (RyR1) (RYR-1) (Skeletal muscl 1 O95672 Endothelin-converting enzyme-like 1 (EC 3.4.24.-) (Xce protein) 1 P22223 Cadherin-3 precursor (Placental-cadherin) (P-cadherin) 1 P22234 Multifunctional protein ADE2 [Includes: Phosphoribosylaminoimidazole-succinocarboxamide syn 1 O95453 Poly(A)-specific ribonuclease (PARN protein) 1 O60566 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta (EC 2.7.1.37) (hBUBR1) (MAD3/ 1 P20618 Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome component C5) (Macropain subunit C5 1 O95777 U6 snRNA-associated Sm-like protein LSm8 1 O95714 HERC2 protein 1 O94880 PHD finger protein 14 1 P26367 Paired box protein Pax-6 (Oculorhombin) (Aniridia, type II protein) 1 P26447 S100 calcium-binding protein A4 (Metastasin) (Mts1 protein) (Placental calcium-binding protein 1 P26639 Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS) 1 O94872 KIAA0774 protein (Fragment) 1 O95271 Tankyrase 1 (EC 2.4.2.30) (TANK1) (Tankyrase I) (TNKS-1) (TRF1-interacting ankyrin-related A 1 P23434 H protein, mitochondrial precursor 1 O95243 Methyl-CpG binding protein 4 (EC 3.2.2.-) (Methyl-CpG binding domain protein 4) (Methyl-CpG b 1 P01771 Ig heavy chain V-III region HIL 1 P13667 Protein disulfide-isomerase A4 precursor (EC 5.3.4.1) (Protein ERp-72) (ERp72) 1 P13637 Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3.9) (Sodium pump 3) (Na+/K+ AT 1 P13942 Collagen alpha 2(XI) chain precursor 1 P01137 Transforming growth factor beta 1 precursor (TGF-beta 1) 1 P01767 Ig heavy chain V-III region BUT 1 P13533 Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha) 1 P01009 Alpha-1-antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase) (PRO0684/ 1 P40616 ADP-ribosylation factor-like protein 1 1 P36952 Maspin precursor (Protease inhibitor 5) 1 O75427 Leucine-rich repeats and calponin homology domain containing protein 4 (Leucine-rich neuronal 1 P38935 DNA-binding protein SMUBP-2 (Immunoglobulin mu binding protein 2) (SMUBP-2) (Glial factor- 1 O75051 KIAA0463 protein (Fragment) 1 O75037 Kinesin family member 21B (Fragment) 1 O60888 Divalent cation tolerant protein CUTA (DJ570F3.2) (LOC51596 (Divalent cation tolerant prote 1 O75154 Eferin 1 P43897 Elongation factor Ts, mitochondrial precursor (EF-Ts) (EF-TsMt) 1 O75912 Diacylglycerol kinase, iota (EC 2.7.1.107) (Diglyceride kinase) (DGK-iota) (DAG kinase iota) 1 P29966 Myristoylated alanine-rich C-kinase substrate (MARCKS) (Protein kinase C substrate, 80 kDa p 1 P30622 Restin (Cytoplasmic linker protein-170 alpha-2) (CLIP-170) (Reed-Sternberg intermediate filam 1 O75923 Dysferlin (Dystrophy associated fer-1-like protein) (Fer-1 like protein 1) 1 P27694 Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A) (Replication factor-A protein 1 P27708 CAD protein [Includes: -dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspa 1 P04275 Von Willebrand factor precursor (vWF) [Contains: Von Willebrand antigen II] 1 P29218 Inositol-1(or 4)-monophosphatase (EC 3.1.3.25) (IMPase) (IMP) (Inositol monophosphatase) (Lit 1 O75995 SH3 protein expressed in lymphocytes homolog 1 P10909 Clusterin precursor (Complement-associated protein SP-40,40) (Complement cytolysis inhibitor 1 P35052 Glypican-1 precursor 1 O75821 Eukaryotic translation initiation factor 3 subunit 4 (eIF-3 delta) (eIF3 p44) (eIF-3 RNA-bindin 1 P35754 Glutaredoxin (Thioltransferase) (TTase) 1 P32780 TFIIH basal transcription factor complex p62 subunit (Basic transcription factor 62 kDa subu 1 P33241 Lymphocyte-specific protein 1 (Protein pp52) (52 kDa phosphoprotein) (Lymphocyte-specific an 1 P10912 Growth hormone receptor precursor (GH receptor) (Somatotropin receptor) [Contains: Growth 1 P31645 Sodium-dependent serotonin transporter (5HT transporter) (5HTT) 1 Q9GZU1 Mucolipin 1 (Mucolipidin) (MG-2) (MSTP080) 1 Q9C0K0 B-cell lymphoma/leukemia 11B (B-cell CLL/lymphoma 11B) (Radiation-induced tumor suppressor g 1 Q9H2E6 Semaphorin 6A precursor (Semaphorin VIA) (Sema VIA) (Semaphorin 6A-1) (SEMA6A-1) 1 Q9H2J1 AD038 1 Q9H2K0 DC38 (Mitochondrial translational initiation factor 3) 1 Q9H372 PRO1433 1 Q9H3C7 C3HC4-type zinc finger protein 1 Q9NP95 Fibroblast growth factor-20 (FGF-20) 1 Q9BVG3 Hypothetical protein FLJ10759 (Novel protein) 1 Q9BXT8 RING finger protein 17 1 Q9GZM6 Olfactory receptor 8D2 (Olfactory receptor-like protein JCG2) 1 Q9C0C8 KIAA1735 protein (Fragment) 1 Q9C0D7 KIAA1726 protein (Fragment) 1 Q9H9P2 Chondrolectin precursor (Transmembrane protein MT75) (Protein PRED12) (UNQ872/PRO1890 1 Q9HBH1 , mitochondrial precursor (EC 3.5.1.88) (PDF) (Polypeptide deformylase) 1 Q9HCU4 Cadherin EGF LAG seven-pass G-type receptor 2 precursor (Epidermal growth factor-like 2) (M 1 Q9NP31 SH2 domain protein 2A (T cell-specific adapter protein) (TSAd) (VEGF receptor-associated pr 1 Q9H4M9 EH-domain containing protein 1 (Testilin) (hPAST1) 1 Q9H559 BA526D8.4 (Novel KRAB box containing C2H2 type zinc finger protein) (Fragment) 1 Q9H598 Vesicular inhibitory amino acid transporter (GABA and glycine transporter) (Vesicular GABA tr 1 Q9H5I1 Histone-lysine N-methyltransferase, H3 lysine-9 specific 2 (EC 2.1.1.43) (Histone H3-K9 methy 1 Q9H5L4 Hypothetical protein FLJ23323 1 Q9H6B0 Hypothetical protein FLJ22422 1 Q9H7L9 FLJ00052 protein (Fragment) 1 Q9H7T0 Hypothetical protein FLJ14298 1 Q96LZ7 Hypothetical protein FLJ32954 1 Q96MH4 Hypothetical protein FLJ32377 1 Q96MM0 Hypothetical protein FLJ32172 1 Q96MN5 Hypothetical protein FLJ32112 (Novel protein) 1 Q96NW3 FLJ00054 protein (Fragment) 1 Q96Q34 ALS2CR13 protein (Fragment) 1 Q96QE2 Proton myo-inositol cotransporter (H(+)-myo-inositol cotransporter) (Hmit) 1 Q96FQ6 S100 calcium-binding protein A16 (S100F) 1 Q96G46 Hypothetical protein LOC56931 1 Q96HP4 Hypothetical protein MGC15763 1 Q96LZ2 Hypothetical protein FLJ32965 1 Q96I99 Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.4) (Succinyl-C 1 Q96QX3 BA54H7.1 (KIAA0865 protein) (Fragment) 1 Q96IF6 FBF1 protein (Fragment) 1 Q96JH7 Deubiquitinating protein VCIP135 (EC 3.4.22.-) (Valosin-containing protein p97/p47 complex-int 1 Q96K72 Hypothetical protein FLJ14464 1 Q9BQA8 G patch domain and KOW motifs 1 Q99733 Nucleosome assembly protein 1-like 4 (Nucleosome assembly protein 2) (NAP2) 1 Q9BPU6 related protein-5 (DRP-5) (ULIP6 protein) (Collapsin response mediator pr 1 Q9BQ15 Hypothetical protein MGC2731 1 Q96QK1 Vacuolar protein sorting 35 (Vesicle protein sorting 35) (hVPS35) (Maternal-embryonic 3) 1 Q9BRJ2 39S ribosomal protein L45, mitochondrial precursor (L45mt) (MRP-L45) 1 Q9BSE5 , mitochondrial precursor (EC 3.5.3.11) ( ) (AUH) 1 Q9BSL1 Ubiquitin associated domain containing 1 (OTTHUMP00000022563) 1 Q96RZ0 Hypothetical protein gs103 1 Q99496 DinG protein (Ring finger protein BAP-1) (Ring finger protein 2) (OTTHUMP00000060668) 1 Q99575 Ribonucleases P/MRP protein subunit POP1 (EC 3.1.26.5) (hPOP1) 1 Q99650 Oncostatin-M specific receptor beta subunit 1 Q9UNL2 Translocon-associated protein, gamma subunit (TRAP-gamma) (Signal sequence receptor gamma 1 Q9UQ80 Proliferation-associated protein 2G4 (Cell cycle protein p38-2G4 homolog) (hG4-1) 1 Q9UQB3 delta-2 (Delta-catenin) (Neural -related ARM-repeat protein) (NPRAP) (Neu 1 Q9Y228 TRAF3-interacting JNK-activating modulator 1 Q9Y250 putative tumor suppressor 1 (F37/esophageal cancer-related gene-coding leucin 1 Q9UJW8 Zinc finger protein 180 (HHZ168) 1 Q9UKE5 TRAF2 and NCK interacting kinase (EC 2.7.1.37) 1 Q9UL04 Membrane protein CH1 1 Q9UL62 Short transient receptor potential channel 5 (TrpC5) (Htrp-5) (Htrp5) 1 Q9ULZ3 Apoptosis-associated speck-like protein containing a CARD (hASC) (PYD and CARD domain cont 1 Q9Y4I1 Myosin Va (Myosin 5A) (Dilute myosin heavy chain, non-muscle) (Myosin heavy chain 12) (Myoxin 1 Q9Y5G7 Protocadherin gamma A6 precursor (PCDH-gamma-A6) 1 Q9Y6C2 EMILIN 1 precursor (Elastin microfibril interface-located protein 1) (Elastin microfibril interf 1 Q9Y3B1 Protein C20orf45 (CGI-107) 1 Q9Y285 Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (--tRNA ligase alpha chain 1 Q9Y2E3 KIAA0931 protein (Fragment) 1 Q9Y305 Putative acyl-CoA thioester hydrolase CGI-16 (EC 3.1.2.-) 1 Q9Y3P9 Rab6 GTPase activating protein, GAPCenA (RABGAP1 protein) (OTTHUMP00000022081) 1 Q9Y3R0 Glutamate receptor-interacting protein 1 (GRIP1 protein) 1 Q9Y3R5 Protein C21orf5 1 Q9Y4D7 Plexin D1 precursor 1 Q9NVS3 Hypothetical protein FLJ10547 1 Q9NY59 Neutral sphingomyelinase II (EC 3.1.4.12) 1 Q9NY74 ETAA16 protein 1 Q9NYI0 Pleckstrin and Sec7 domain containing protein 3 (Exchange factor for ADP-ribosylation factor 1 Q9NYV9 Taste receptor type 2 member 13 (T2R13) (Taste receptor family B member 3) (TRB3) 1 Q9NQ87 HEYL protein (Hairy/enhancer-of-split related with YRPW motif-like) (Hairy-related transcrip 1 Q9NQW6 Actin binding protein anillin 1 Q9NU39 Forkhead box protein D4-like 1 1 Q9NV16 Hypothetical protein FLJ10993 1 Q9NV64 Hypothetical protein FLJ10902 1 Q9UBV7 Beta-1,4-galactosyltransferase 7 (EC 2.4.1.-) (Beta-1,4-GalTase 7) (Beta4Gal-T7) (b4Gal-T7) (U 1 Q9UHP6 Rhabdoid tumor deletion region protein 1 1 Q9UI33 Sodium channel protein type XI alpha subunit (Voltage-gated sodium channel alpha subunit Nav 1 Q96EP1 Ubiquitin ligase protein CHFR (EC 6.3.2.-) (Checkpoint with forkhead and RING finger domains 1 Q9NZM3 Intersectin 2 (SH3 domain-containing protein 1B) (SH3P18) (SH3P18-like WASP associated pro 1 Q9NZT2 Opioid growth factor receptor (OGFr) (Zeta-type opioid receptor) (7-60 protein) 1 Q9NZV1 Cysteine-rich repeat-containing protein S52 precursor (CRIM1) 1 Q9P0K8 Forkhead box protein J2 (Fork head homologous X) 1 Q9P0M7 HSPC252 1 Q9P2I6 KIAA1361 protein (Fragment) 1 Q9P2Y5 UV radiation resistance-associated gene protein (p63) 1 Q9UBC3 DNA (cytosine-5)-methyltransferase 3B (EC 2.1.1.37) (Dnmt3b) (DNA methyltransferase HsaI 1 Q9NZ56 Formin 2 (Fragments) 1 Q6ZTV6 Hypothetical protein FLJ44186 1 Q6ZU73 Hypothetical protein FLJ43954 1 Q6ZUZ4 Hypothetical protein FLJ43187 1 Q6ZVC0 Hypothetical protein FLJ42783 1 Q6ZVY7 Hypothetical protein FLJ41907 1 Q86XJ2 PLCL4 protein (Fragment) 1 Q6ZRL9 Hypothetical protein FLJ46257 1 Q6ZSR9 Hypothetical protein FLJ45252 1 Q86SJ2 Amphoterin induced gene 2 (DEGA/AMIGO-2 precursor) (Alivin 1) (Transmembrane protein AM 1 Q86U33 Full-length cDNA clone CS0DA005YA22 of Neuroblastoma of Homo sapiens (human) (Fragment 1 Q86VH3 Hypothetical protein 1 Q86U54 CD151 antigen (CD151 protein) 1 Q76E58 Epiplakin 1 Q7Z2W7 Transient receptor potential cation channel subfamily M member 8 (Transient receptor potent 1 Q7Z7L7 Chromosome 9 open reading frame 60 (OTTHUMP00000022294) 1 Q7Z6K5 Similar to mouse 2610034B18Rik protein 1 Q7Z707 DJ1042K10.5 (Novel protein) (Fragment) 1 Q7Z727 Hypothetical protein (Fragment) 1 Q5VX49 OTTHUMP00000030575 1 Q5VZR4 Hippocampus abundant gene transcript-like 2 1 Q68CR0 Hypothetical protein DKFZp781K12107 (Fragment) 1 Q15057 Centaurin beta 2 (Cnt-b2) 1 Q15058 Kinesin-like protein KIF14 1 Q15361 Transcription factor 1 Q15662 Transformation-related protein (Fragment) 1 Q15782 Chitinase 3-like protein 2 precursor (YKL-39) (Chondrocyte protein 39) 1 Q15884 Protein C9orf61 (Protein X123) (Fragment) 1 Q6P9G8 Chromosome 6 open reading frame 60 1 Q6PJI4 CBF1 interacting corepressor, isoform 2 1 Q6XYD6 LP2477 1 Q6ZNC2 Hypothetical protein FLJ16223 1 Q6IS24 Putative polypeptide N-acetylgalactosaminyltransferase-like protein 3 (EC 2.4.1.41) (Protein-UD 1 Q6ZNE3 Hypothetical protein FLJ16182 1 Q68DN1 Hypothetical protein DKFZp781D2023 1 Q69YQ3 Hypothetical protein DKFZp762I052 (OTTHUMP00000064740) 1 Q6AI58 Hypothetical protein DKFZp781A0295 (Fragment) 1 Q6IQ22 Hypothetical protein (Fragment) 1 Q6P3W7 Similar to mouse D10Ertd802e protein 1 Q6MZZ7 Hypothetical protein DKFZp686L13193 1 Q6NZI2 Polymerase I and transcript release factor (PTRF protein) (FKSG13 protein) 1 Q8TB37 Protein C14orf127 1 Q8TB91 Prospero-related homeobox 1 1 Q96BJ8 Engulfment and cell motility protein 3 1 Q969X1 RECS1 protein homolog (PP1201) 1 Q96A40 Hypothetical protein FLJ30760 (Paraneoplastic antigen like 6A) 1 Q96AA8 Hypothetical protein KIAA0555 1 Q96CT7 Hypothetical protein LOC115098 1 Q96DY7 Mdm2, transformed 3T3 cell double minute 2, binding protein binding protein 1 Q92598 Heat-shock protein 105 kDa (Heat shock 110 kDa protein) (Antigen NY-CO-25) 1 Q8WYX4 Hypothetical protein pp11662 1 Q92484 Acid sphingomyelinase-like phosphodiesterase 3a precursor (EC 3.1.4.-) (ASM-like phosphodiest 1 Q92542 Nicastrin precursor (UNQ1874/PRO4317) 1 Q93097 Wnt-2b protein precursor (Wnt-13) 1 Q92772 P56 KKIAMRE protein kinase 1 Q92890 Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1) 1 Q92562 Protein KIAA0274 1 Q8N158 Glypican 2 (Hypothetical protein FLJ38962) (Hypothetical protein DKFZp547M109) 1 Q8N3F8 Molecule interacting with Rab13 (MIRab13) (MICAL-like protein 1) 1 Q8N3R9 MAGUK p55 subfamily member 5 1 Q8N3T1 Polypeptide N-acetylgalactosaminyltransferase-like protein 2 (EC 2.4.1.41) (Protein-UDP acetyl 1 Q8N4B6 Chromosome 6 open reading frame 10 1 Q8IW25 Hypothetical protein KIAA1586 (OTTHUMP00000040022) 1 Q8IVU3 HERC6 protein (Fragment) 1 Q8N655 Chromosome 10 open reading frame 12 1 Q8IW72 LOC374654 protein (Fragment) 1 Q8IXL7 LOC253827 protein 1 Q8IY92 BTB/POZ domain containing protein 12 1 Q8NC44 Hypothetical protein FLJ90502 1 Q8NC75 Hypothetical protein FLJ90437 1 Q8NCA5 Hypothetical protein FLJ90386 1 Q8NCN4 KIAA1991 protein (Fragment) 1 Q8NBN0 Hypothetical protein PSEC0101 1 Q8NFJ9 Bardet-Biedl syndrome 1 protein (BBS2-like protein 2) 1 Q8NFN8 GABAB-related G-protein coupled receptor 1 Q8NG48 WINS1 protein with Drosophila Lines (Lin) homologous domain 1 Q8NA27 Hypothetical protein FLJ35908 1 Supplemental Table 4: Proteins identified only in poorly differentiated HNSCC

Peptides Accession Protein (number) Q6ZVY6 Hypothetical protein FLJ41910 8 Q13015 Protein AF1q 6 P23526 (EC 3.3.1.1) (S-adenosyl-L-homocysteine hydrolase) (AdoHcyase) 4 P31040 [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) (Fl 4 Q96FV1 KRT19 protein (Fragment) 4 Q9UJS0 Calcium-binding protein Aralar2 (Mitochondrial aspartate glutamate carrier 2) (So 4 P36542 ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14) 3 O43143 Putative pre-mRNA splicing factor RNA helicase (DEAH box protein 15) (ATP-dependent RNA helicase # 2 P51648 Fatty aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase, microsomal) (ALDH class 3) 2 P49736 DNA replication licensing factor MCM2 (Minichromosome maintenance protein 2 homolog) (Nuclear prot 2 Q13263 Transcription intermediary factor 1-beta (TIF1-beta) (Tripartite motif protein 28) (Nuclear corepresso 2 Q13423 NAD(P) transhydrogenase, mitochondrial precursor (EC 1.6.1.2) (Pyridine nucleotide transhydrogenase) ( 2 Q08397 Lysyl oxidase homolog 1 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 1) (LOL) 2 P00352 Aldehyde dehydrogenase 1A1 (EC 1.2.1.3) (Aldehyde dehydrogenase, cytosolic) (ALDH class 1) (Retinal d 2 P09936 Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12) (UCH-L1) (Ubiquitin thiolesterase L1) (N 2 O94826 Mitochondrial precursor proteins import receptor ( of outer membrane TOM70) 2 P43652 Afamin precursor (Alpha-albumin) (Alpha-Alb) 2 P33992 DNA replication licensing factor MCM5 (CDC46 homolog) (P1-CDC46) 2 Q9BZD6 Transmembrane gamma-carboxyglutamic acid protein 4 precursor (Proline-rich Gla protein 4) (Proline-ri 2 Q9BZE4 Nucleolar GTP-binding protein 1 (Chronic renal failure gene protein) (GTP-binding protein NGB) 2 Q9H977 Hypothetical protein FLJ12953 2 Q9HB21 Pleckstrin homology domain-containing A member 1 (Tandem PH domain containing protein 2 Q96R06 Sperm associated antigen 5 (Astrin) (Mitotic spindle associated protein p126) (MAP126) (Deepest) 2 Q9NU22 Midasin (MIDAS-containing protein) 2 Q9UGU0 Transcription factor 20 (Stromelysin 1 PDGF-responsive element-binding protein) (SPRE-binding protein 2 Q9UHB6 Epithelial protein lost in neoplasm 2 Q6P4U5 2 Q8IWU9 5-hydroxylase 2 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 2) (Neuronal tryptophan hydr 2 Q8NB12 SET and MYND domain containing protein 1 2 P08648 Integrin alpha-5 precursor (Fibronectin receptor alpha subunit) (Integrin alpha-F) (VLA-5) (CD49e) 1 O43402 Neighbor of COX4 1 O43396 Thioredoxin-like protein 1 (32 kDa thioredoxin-related protein) 1 P60900 Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome iota chain) (Macropain iota chain) (Multicata 1 O43324 Multisynthetase complex auxiliary component p18 1 O43464 Serine protease HTRA2, mitochondrial precursor (EC 3.4.21.-) (High temperature requirement protein A 1 P61106 Ras-related protein Rab-14 1 O43490 Prominin 1 precursor (Prominin-like protein 1) (Antigen AC133) (CD133 antigen) 1 P63208 S-phase kinase-associated protein 1A (Cyclin A/CDK2-associated protein p19) (p19A) (p19skp1) (RNA po 1 P62888 60S ribosomal protein L30 1 P08397 Porphobilinogen deaminase (EC 2.5.1.61) (Hydroxymethylbilane synthase) (HMBS) (Pre-uroporphyrinogen 1 P62879 Guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2 (Transducin beta chain 2) (G protein b 1 O60296 Amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 3 1 P51610 Host cell factor C1 (HCF) (VP16 accessory protein) (HFC1) (VCAF) (CFF) 1 P51649 Succinate semialdehyde dehydrogenase, mitochondrial precursor (EC 1.2.1.24) (NAD(+)-dependent succi 1 P49720 Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome theta chain) (Proteasome chain 13) (Proteaso 1 P49748 Acyl-CoA dehydrogenase, very-long-chain specific, mitochondrial precursor (EC 1.3.99.-) (VLCAD) 1 P55084 Trifunctional enzyme beta subunit, mitochondrial precursor (TP-beta) (MSTP029) [Includes: 3-ketoacyl 1 P53999 Activated RNA polymerase II transcriptional coactivator p15 (Positive cofactor 4) (PC4) (p14) 1 P55769 NHP2-like protein 1 (High mobility group-like nuclear protein 2 homolog 1) ([U4/U6.U5] tri-snRNP 15.5 k 1 P56192 Methionyl-tRNA synthetase (EC 6.1.1.10) (--tRNA ligase) (MetRS) 1 P80404 4-aminobutyrate aminotransferase, mitochondrial precursor (EC 2.6.1.19) ((S)-3-amino-2-methylpropion 1 O00560 Syntenin 1 (Syndecan binding protein 1) (Melanoma differentiation associated protein-9) (Mda-9) (Scaff 1 Q13424 Alpha-1-syntrophin (59 kDa -associated protein A1, acidic component 1) (Pro-TGF-alpha cytop 1 Q12959 Presynaptic protein SAP97 (Synapse-associated protein 97) (Discs, large homolog 1) (hDlg) 1 O00461 130 kD Golgi-localized phosphoprotein 1 O00625 Pirin 1 P07099 Epoxide hydrolase 1 (EC 3.3.2.3) (Microsomal epoxide hydrolase) (Epoxide hydratase) 1 O00217 NADH-ubiquinone oxidoreductase 23 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Co 1 O00308 Nedd-4-like E3 ubiquitin-protein ligase WWP2 (EC 6.3.2.-) (WW domain-containing protein 2) (Atropin- 1 O00154 Cytosolic acyl coenzyme A thioester hydrolase (EC 3.1.2.2) (Long chain acyl-CoA thioester hydrolase) (C 1 O00366 Putative p150 1 Q14139 Ubiquitin conjugation factor E4 A 1 Q14166 Hypothetical protein KIAA0153 1 Q01484 Ankyrin 2 (Brain ankyrin) (Ankyrin B) (Ankyrin, nonerythroid) 1 Q00577 Transcriptional activator protein PUR-alpha (Purine-rich single-stranded DNA-binding protein alpha) 1 Q01668 Voltage-dependent L-type calcium channel alpha-1D subunit (Voltage-gated calcium channel alpha subuni 1 O15305 Phosphomannomutase 2 (EC 5.4.2.8) (PMM 2) 1 P48047 ATP synthase oligomycin sensitivity conferral protein, mitochondrial precursor (EC 3.6.3.14) (OSCP) 1 P08243 synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas 1 O15127 Secretory carrier-associated membrane protein 2 (Secretory carrier membrane protein 2) 1 P84157 Transmembrane anchor protein 1 1 Q08378 Golgi autoantigen, golgin subfamily A member 3 (Golgin-160) (Golgi complex-associated protein of 170 k 1 Q02880 DNA topoisomerase II, beta isozyme (EC 5.99.1.3) 1 Q02338 D-beta-hydroxybutyrate dehydrogenase, mitochondrial precursor (EC 1.1.1.30) (BDH) (3-hydroxybutyra 1 O14979 JKTBP2 (Heterogeneous nuclear ribonucleoprotein D-like) (HNRPDL protein) 1 O14896 Interferon regulatory factor 6 (IRF-6) 1 Q04637 Eukaryotic translation initiation factor 4 gamma 1 (eIF-4-gamma 1) (eIF-4G1) (eIF-4G) (p220) 1 Q02790 FK506-binding protein 4 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotamase) (p59 prot 1 P20396 Thyroliberin precursor (Thyrotropin releasing hormone) (TRH) (Thyrotropin releasing factor) (TSH-rele 1 P21796 Voltage-dependent anion-selective channel protein 1 (VDAC-1) (hVDAC1) (Outer mitochondrial membran 1 O95861 3'(2'),5'-bisphosphate nucleotidase 1 (EC 3.1.3.7) (Bisphosphate 3'-nucleotidase 1) (PAP-inositol-1,4-pho 1 P11117 Lysosomal acid phosphatase precursor (EC 3.1.3.2) (LAP) 1 P25092 Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal guanylate cyclase) (EC 4.6.1.2) (STA rec 1 P25205 DNA replication licensing factor MCM3 (DNA polymerase alpha holoenzyme-associated protein P1) (RLF 1 P26196 Probable ATP-dependent RNA helicase p54 (Oncogene RCK) (DEAD-box protein 6) 1 O95295 SNARE-associated protein Snapin (Synaptosomal-associated protein 25 binding protein) (SNAP-associa 1 O94947 KIAA0870 protein (Fragment) 1 P13674 Prolyl 4-hydroxylase alpha-1 subunit precursor (EC 1.14.11.2) (4-PH alpha-1) (Procollagen-proline,2-oxogl 1 P11586 C-1-tetrahydrofolate synthase, cytoplasmic (C1-THF synthase) [Includes: Methylenetetrahydrofolate d 1 P12277 , B chain (EC 2.7.3.2) (B-CK) 1 P13521 Secretogranin II precursor (SgII) (Chromogranin C) [Contains: Secretoneurin (SN)] 1 P00797 Renin precursor (EC 3.4.23.15) (Angiotensinogenase) 1 P17844 Probable RNA-dependent helicase p68 (DEAD-box protein p68) (DEAD-box protein 5) 1 P11226 Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) 1 P19404 NADH-ubiquinone oxidoreductase 24 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) 1 P16415 Zinc finger protein ZFP-36 (Fragment) 1 P11388 DNA topoisomerase II, alpha isozyme (EC 5.99.1.3) 1 P17050 Alpha-N-acetylgalactosaminidase precursor (EC 3.2.1.49) (Alpha-galactosidase B) 1 P11277 Spectrin beta chain, erythrocyte (Beta-I spectrin) 1 P17538 Chymotrypsinogen B precursor (EC 3.4.21.1) 1 P10253 Lysosomal alpha-glucosidase precursor (EC 3.2.1.20) (Acid maltase) 1 P40227 T-complex protein 1, zeta subunit (TCP-1-zeta) (CCT-zeta) (CCT-zeta-1) (Tcp20) (HTR3) (Acute morphin 1 P40617 ADP-ribosylation factor-like protein 4A 1 O75396 Vesicle trafficking protein SEC22b (SEC22 vesicle trafficking protein-like 1) 1 O75340 Programmed cell death protein 6 (Probable calcium-binding protein ALG-2) 1 O75351 SKD1 protein (Vacuolar sorting protein 4b) 1 P09874 Poly [ADP-ribose] polymerase-1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase-1) (Pol 1 P42768 Wiskott-Aldrich syndrome protein (WASp) 1 P30040 Endoplasmic reticulum protein ERp29 precursor (ERp31) (ERp28) 1 P30050 60S ribosomal protein L12 1 P30084 Enoyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.17) (Short chain enoyl-CoA hydratase) (SCEH) ( 1 O76095 JTB protein precursor (Jumping translocation breakpoint protein) (Prostate androgen regulated protein 1 O75932 SYT interacting protein SIP (RBM14 protein) 1 P33993 DNA replication licensing factor MCM7 (CDC47 homolog) (P1.1-MCM3) 1 P35348 Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergi 1 P04632 Calpain small subunit 1 (CSS1) (Calcium-dependent protease small subunit 1) (Calcium-dependent proteas 1 O75489 NADH-ubiquinone oxidoreductase 30 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Co 1 O75592 Protein associated with Myc 1 P31939 Bifunctional purine biosynthesis protein PURH (OK/SW-cl.86) [Includes: Phosphoribosylaminoimidazolec 1 P32969 60S ribosomal protein L9 1 O75667 N-acetylglucosamine-6-O-sulfotransferase (Carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 1 Q9H492 Microtubule-associated proteins 1A/1B light chain 3A (MAP1A/MAP1B LC3 A) (MAP1A/1B light chain 3 A 1 Q9H053 Hypothetical protein DKFZp547K202 (Fragment) 1 Q9H0I3 Hypothetical protein DKFZp434N1418 (HSPC065 protein) 1 Q9H2A2 Aldehyde dehydrogenase 12 (OTTHUMP00000040210) 1 Q9BUN8 Derlin-1 (Degradation in endoplasmic reticulum protein 1) (Der1-like protein 1) (DERtrin 1) (UNQ243/PR 1 Q9BVA7 DKFZP586B1621 protein 1 Q9BY66 Jumonji/ARID domain-containing protein 1D (SmcY protein) (Histocompatibility Y antigen) (H-Y) 1 Q9BYN7 Zinc finger protein 341 1 Q9BZ74 FKSG42 1 Q9C0C2 182 kDa tankyrase 1-binding protein 1 Q9H9B4 Sideroflexin 1 1 Q9H9L9 Hypothetical protein FLJ12664 1 Q9HAU0 Pleckstrin homology domain-containing protein family A member 5 (Phosphoinositol 3-phosphate-binding 1 Q9HCL7 KIAA1555 protein (Fragment) 1 Q9H4E7 Def-6 protein (OTTHUMP00000039602) 1 Q9BU59 Smu-1 suppressor of mec-8 and unc-52 homolog (OTTHUMP00000045234) 1 Q9H721 Hypothetical protein FLJ21497 1 Q9H7Z0 Hypothetical protein FLJ14058 1 Q96MM6 Heat shock 70 kDa protein 12B 1 Q96L91 E1A binding protein p400 (EC 3.6.1.-) (p400 kDa SWI2/SNF2-related protein) (Domino homolog) (hDom 1 Q96P70 Importin 9 (Imp9) (Ran-binding protein 9) (RanbP9) (HSPC273) 1 Q96PY5 KIAA1902 protein (Fragment) 1 Q96IF1 JUB protein (Ajuba) (Jub, ajuba homolog, isoform 1) 1 Q96K26 Hypothetical protein FLJ14834 1 Q9BPX5 Actin related protein 2/3 complex, subunit 5-like 1 Q9BQA2 T1 protein 1 Q99684 Zinc finger protein Gfi-1 (Growth factor independence-1) 1 Q9BQE5 Apolipoprotein L2 (Apolipoprotein L-II) (ApoL-II) 1 Q9BQJ1 Hypothetical protein DKFZp761G0712 1 Q9BS43 Chromosome 14 open reading frame 168 1 Q9BT43 Hypothetical protein MGC3200 (Hypothetical protein FLJ32422) 1 Q9BTV7 Cdk5 and abl enzyme substrate 2 (Interactor with cdk3 2) (Ik3-2) 1 Q9NQ11 Probable cation-transporting ATPase 1 (EC 3.6.3.-) 1 Q99415 AAD14 protein (Fragment) 1 Q96S08 Some homology with holliday junction DNA helicase RUVB like 1 Q96S23 Hypothetical protein RJD1 1 Q96ST8 Hypothetical protein FLJ14640 1 Q99460 26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S prot 1 Q99627 COP9 signalosome complex subunit 8 (Signalosome subunit 8) (SGN8) (JAB1-containing signalosome subu 1 Q96SA0 Hypothetical protein 1 Q9UQ49 Sialidase 3 (EC 3.2.1.18) (Membrane sialidase) (Ganglioside sialidase) (N-acetyl-alpha-neuraminidase 3) 1 Q9UMS4 PRP19/PSO4 homolog (Nuclear matrix protein 200) (hPso4) 1 Q9Y230 RuvB-like 2 (EC 3.6.1.-) (48-kDa TATA box-binding protein-interacting protein) (48-kDa TBP-interacting 1 Q9NP90 Ras-related protein Rab-9B (Rab-9L) (RAB9-like protein) 1 Q9UL25 Ras-related protein Rab-21 1 Q9ULK4 Cofactor required for Sp1 transcriptional activation subunit 3 (Transcriptional coactivator CRSP130) (V 1 Q9Y5U9 HSPC039 protein (Hypothetical transmembrane protein) (Immediate early response 3 interacting prote 1 Q9Y259 Choline/ethanolamine kinase [Includes: Choline kinase beta (EC 2.7.1.32) (CK); Ethanolamine kinase (EC 2 1 Q9Y4K4 Mitogen-activated protein kinase kinase kinase kinase 5 (EC 2.7.1.37) (MAPK/ERK kinase kinase kinase 5 1 Q9Y5S8 NADPH oxidase homolog 1 (NOX-1) (NOH-1) (NADH/NADPH mitogenic oxidase subunit P65-MOX) (Mit 1 Q9Y4F1 CDEP (FERM, RhoGEF, and pleckstrin domain protein 1, isoform 1) (FERM, RhoGEF (ARHGEF) and plecks 1 Q9Y694 Liver-specific transporter (Solute carrier family 22 member 7, isoform a) (OTTHUMP00000016429) (O 1 Q9Y6E7 NAD-dependent deacetylase sirtuin 4 (EC 3.5.1.-) (SIR2-like protein 4) 1 Q9Y2P0 BC37295_3 1 Q9Y2U8 Inner nuclear membrane protein Man1 (LEM domain containing protein 3) 1 Q9Y333 U6 snRNA-associated Sm-like protein LSm2 (SnRNP core Sm-like protein Sm-x5) (G7b protein) (Small n 1 Q9Y3D9 Mitochondrial ribosomal protein S23 (S23mt) (MRP-S23) (CGI-138) (HSPC329) 1 Q9Y485 X-like 1 protein 1 Q9Y314 CGI-25 protein (ENOS interacting protein) 1 Q9NVX0 Centrosomal protein of 27 kDa (Cep27 protein) 1 Q9NVK9 Hypothetical protein FLJ10665 1 Q9NY15 Stabilin 1 precursor (FEEL-1 protein) (MS-1 antigen) 1 Q9NQ38 Serine protease inhibitor Kazal-type 5 precursor (Lympho-epithelial Kazal-type related inhibitor) (LEKT 1 Q9NQT8 Kinesin-like protein KIF13B (Kinesin-like protein GAKIN) 1 Q9NRW7 Vacuolar protein sorting-associated protein 45 (h-VPS45) (hlVps45) 1 Q9NS69 Mitochondrial import receptor subunit TOM22 homolog (Translocase of outer membrane 22 kDa subunit 1 Q9NTG1 Polycystic kidney disease and receptor for egg jelly related protein precursor (PKD and REJ homolog) 1 Q9UBU7 Activator of S phase Kinase (Dbf4 protein) 1 Q9UII5 Zinc finger protein ZFD25 1 Q9NZD2 Glycolipid transfer protein (GLTP) 1 Q9P202 Whirlin (Autosomal recessive deafness type 31 protein) 1 Q9P253 Vacuolar protein sorting 18 (hVPS18) 1 Q9P2D0 KIAA1417 protein (Fragment) 1 Q9UBB5 Methyl-CpG binding protein 2 (Methyl-CpG binding domain protein 2) (Demethylase) (DMTase) 1 Q6ZU28 Hypothetical protein FLJ44037 1 Q6ZTF8 Hypothetical protein FLJ44700 1 Q70EK9 Ubiquitin carboxyl-terminal hydrolase 51 (EC 3.1.2.15) (Ubiquitin thiolesterase 51) (Ubiquitin-specific pr 1 Q6ZVA7 Hypothetical protein FLJ42816 1 Q6ZQP9 Hypothetical protein FLJ46332 1 Q6ZS40 Hypothetical protein FLJ45856 1 Q6ZSC0 Hypothetical protein FLJ45651 1 Q712M9 Serotonin receptor 5-HT4 1 Q86TI6 Hypothetical protein 1 Q7Z7C1 E3 ubiquitin ligase 1 Q86UP2 Kinectin (Kinesin receptor) (CG-1 antigen) 1 Q86UX7 Unc-112 related protein 2 (Kindlin-3) (MIG2-like) 1 Q86VG6 Hypothetical protein 1 Q71S18 (Fragment) 1 Q5VWB1 OTTHUMP00000059958 (Sorting nexin family member 27) 1 Q6ZNH7 Hypothetical protein FLJ16074 1 Q16718 NADH-ubiquinone oxidoreductase 13 kDa-B subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-13Kd-B) (CI-13 1 Q16719 (EC 3.7.1.3) (L- hydrolase) 1 Q16795 NADH-ubiquinone oxidoreductase 39 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Co 1 Q16661 Uroguanylin precursor (UGN) (Guanylate cyclase activator 2B) (Guanylate cyclase C activating peptide I 1 Q5VZV1 OTTHUMP00000018663 1 Q659D6 Hypothetical protein DKFZp434O2321 (Fragment) 1 Q66K66 Similar to RIKEN cDNA A230078I05 gene 1 Q15185 Telomerase-binding protein p23 (Hsp90 co-chaperone) ( complex p23) 1 Q16558 Calcium-activated potassium channel beta subunit 1 (Calcium-activated potassium channel, subfamily M, 1 Q6UWI4 Protein UNQ9166/PRO28631 precursor 1 Q6PUV4 Complexin 2 (Synaphin 1) 1 Q6XYB9 FP18315 1 Q6DEN2 DPYSL3 protein 1 Q6FHX4 MAP2K4 protein 1 Q6GMX1 Hypothetical protein 1 Q8TE87 Hypothetical protein FLJ23801 1 Q8TF23 KIAA1979 protein (Fragment) 1 Q8TE58 ADAMTS-15 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 1 1 Q8TF72 Shroom-related protein 1 Q8NGV9 Seven transmembrane helix receptor 1 Q8NHQ1 P10-binding protein 1 Q8WYR1 FOAP-2 1 Q969T9 WW domain binding protein 2 (WBP-2) 1 Q969V1 -concentrating hormone receptor 2 (MCH receptor 2) (MCHR-2) (MCH-R2) (MCH2R) (MCH-2R) 1 Q96BH1 RING finger protein 25 (EC 6.3.2.-) 1 Q96CN9 GRIP and coiled-coil domain-containing protein 1 (Golgi coiled coil protein 1) 1 Q92499 ATP-dependent helicase DDX1 (DEAD-box protein 1) (DEAD-box protein-retinoblastoma) (DBP-RB) 1 Q92522 Histone H1x 1 Q92572 Adapter-related protein complex 3 sigma 1 subunit (Sigma-adaptin 3a) (AP-3 complex sigma-3A subunit) 1 Q92900 Regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppr 1 Q8N262 Hypothetical protein FLJ33880 1 Q8IZ83 Hypothetical protein MGC10204 1 Q8IZQ1 ALFY 1 Q8IZS5 MRDS1 protein (OTTHUMP00000039226) 1 Q8N0U8 epoxide reductase complex, subunit 1-like 1 (VKORC1-like protein 1) 1 Q8IYW6 Hypothetical protein FLJ35808 1 Q8N1Z5 Hypothetical protein FLJ37183 1 Q8N3C2 Hypothetical protein DKFZp761P189 (Fragment) 1 Q8N4H9 MGC39821 protein 1 Q86XZ6 Hypothetical protein (Fragment) 1 Q86YV5 FLJ00269 protein (Fragment) 1 Q8IUD2 ERC protein 1 (ELKS protein) 1 Q8IVL8 Zn-carboxypeptidase 1 Q8IVW4 CDKL3 protein 1 Q8IWA4 Transmembrane GTPase MFN1 (EC 3.6.5.-) (Mitofusin 1) (Fzo homolog) 1 Q8IYA6 Hypothetical protein FLJ40629 1 Q8IVV7 Hypothetical protein C17orf39 1 Q8ND68 Hypothetical protein DKFZp667O074 (Fragment) 1 Q8NDJ2 Hypothetical protein DKFZp547G125 (Fragment) 1 Q8NEV8 Slp homolog lacking C2 domains-b (Exophilin 5) 1 Q8N7Z8 Hypothetical protein FLJ40182 1 Q8N8V2 Hypothetical protein FLJ38822 1 Q8NBP7 Proprotein convertase subtilisin/kexin type 9 precursor (EC 3.4.21.-) (Proprotein convertase PC9) (Subt 1 Q8NAU3 Hypothetical protein FLJ34780 1 Q8N8L4 Hypothetical protein FLJ39262 1 Supplemental Table 5: Proteins identified only in normal and well differentiated HNSCC

Peptides Accession Protein (number) P12821 PIWIL3 protein 9 Q9Y6X9 LOC132200 protein 4 Q86US8 Leukocyte elastase inhibitor (LEI) (Monocyte/neutrophil elastase inhibitor) (M/NEI) (EI) 4 Q8TE73 Glutamate receptor delta-1 subunit precursor (GluR delta-1) 4 Q9HC35 Chromodomain-helicase-DNA-binding protein 6 (CHD-6) 3 Q96RV3 Gamma-synergin 3 Q9UM54 Zinc finger and BTB domain containing protein 4 (KAISO-like zinc finger protein 1) (KAISO- 3 Q68CR2 Testis protein TEX15 2 Q6EH31 Serine/threonine-protein kinase 3 (EC 2.7.1.37) (STE20-like kinase MST2) (MST-2) (Mamma 2 Q8WXQ6 130 kDa leucine-rich protein (LRP 130) (GP130) (Leucine-rich PPR-motif containing protein) 2 Q01546 ALMS1 protein 2 O43175 Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.1.2.15) (Ubiquitin thiolesterase 25) (Ubiquitin 2 Q8TBI2 Apoptotic protease activating factor 1 (Apaf-1) 2 P02768 Importin-alpha re-exporter (Chromosome segregation 1-like protein) (Cellular apoptosis susc 2 O15553 Spermine synthase (EC 2.5.1.22) (Spermidine aminopropyltransferase) (SPMSY) 2 P49792 Calpain 1, large [catalytic] subunit (EC 3.4.22.52) (Calcium-activated neutral proteinase) (CAN 2 P08173 Laminin beta-1 chain precursor (Laminin B1 chain) 2 P15374 Microtubule-associated protein 1B (MAP 1B) [Contains: MAP1 light chain LC1] 2 Q9GZT9 Tyrosine-protein kinase SYK (EC 2.7.1.112) (Spleen tyrosine kinase) 2 Q96EY4 U5 small nuclear ribonucleoprotein 200 kDa helicase (EC 3.6.1.-) (U5 snRNP-specific 200 kDa 2 P28715 Kinesin heavy chain (Ubiquitous kinesin heavy chain) (UKHC) 2 Q9NP61 Echinoderm microtubule-associated protein-like 4 (EMAP-4) (Restrictedly overexpressed pr 2 Q15369 Pecanex-like protein 1 (Pecanex homolog) 2 P07814 Myosin VI 2 Q9H6N6 Zinc finger protein 64, isoforms 3 and 4 (Zinc finger protein 338) 2 P30740 Hypothetical protein FLJ42406 2 Q7Z2Y8 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1) 2 Supplemental Table 6: Proteins identified only in well and mild differentiated HNSCC

Peptides Accession Protein (number) Q13753 Laminin gamma-2 chain precursor (Kalinin/nicein/epiligrin 100 kDa subunit) (Laminin B2t chai 13 P08729 Keratin, type II cytoskeletal 7 (Cytokeratin 7) (K7) (CK 7) (Sarcolectin) 11 P02675 Fibrinogen beta chain precursor [Contains: Fibrinopeptide B] 11 P02647 Apolipoprotein A-I precursor (Apo-AI) (ApoA-I) 9 Q13751 Laminin beta-3 chain precursor (Laminin 5 beta 3) (Laminin B1k chain) (Kalinin B1 chain) 9 P01024 Complement C3 precursor [Contains: C3a anaphylatoxin] 8 P02671 Fibrinogen alpha/alpha-E chain precursor [Contains: Fibrinopeptide A] 8 Q8IVR4 COL23A1 protein 7 Q6ZQN2 Hypothetical protein FLJ46846 7 Q66K23 Hypothetical protein (Fragment) 7 Q9UBI6 Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 subunit 6 P05198 Eukaryotic translation initiation factor 2 subunit 1 (Eukaryotic translation initiation factor 2 6 Q9NQP4 Prefoldin subunit 4 (Protein C-1) 6 P02787 Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1-metal binding globulin) (PRO1 5 P61981 14-3-3 protein gamma (Protein kinase C inhibitor protein-1) (KCIP-1) 5 P50991 T-complex protein 1, delta subunit (TCP-1-delta) (CCT-delta) (Stimulator of TAR RNA bindin 5 P16615 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA 5 Q9NS15 Latent transforming growth factor beta binding protein 3 precursor (LTBP-3) 5 P25815 S-100P protein 5 Q6ZRU0 Hypothetical protein FLJ46111 5 Q13409 Dynein intermediate chain 2, cytosolic (DH IC-2) (Cytoplasmic dynein intermediate chain 2) 5 Q6P9F5 Tripartite motif 40 protein (RING finger protein 35) 5 P20073 Annexin A7 (Annexin VII) (Synexin) (OK/SW-cl.95) 4 P49590 Histidyl-tRNA synthetase homolog (EC 6.1.1.21) (Histidine--tRNA ligase homolog) (HisRS) 4 P25103 Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykinin receptor 1) 4 Q9Y5P3 Retinoic acid-induced protein 2 4 Q8N9V6 Hypothetical protein FLJ36160 4 O75533 Splicing factor 3B subunit 1 (Spliceosome associated protein 155) (SAP 155) (SF3b155) (Pre- 4 Q9H7V7 Hypothetical protein FLJ14207 4 Q86T83 Hypothetical protein DKFZp451J0218 4 P38919 Probable ATP-dependent helicase DDX48 (DEAD-box protein 48) (Eukaryotic initiation facto 4 P16144 Integrin beta-4 precursor (GP150) (CD104 antigen) 4 Q8TD16 Cytoskeleton-like bicaudal D protein homolog 2 3 P48200 Iron-responsive element binding protein 2 (IRE-BP 2) (Iron regulatory protein 2) (IRP2) 3 P41218 Myeloid cell nuclear differentiation antigen 3 Q6NXN2 Hypothetical protein 3 Q86Z22 Hypothetical protein 3 Q8IWJ2 GRIP and coiled-coil domain-containing protein 2 (Golgi coiled coil protein GCC185) (CTCL tum 3 P40818 Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin thiolesterase 8) (Ubiquitin-s 3 P25786 Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome component C2) (Macropain subunit 3 P29034 S100 calcium-binding protein A2 (S-100L protein) (CAN19) 3 Q9BS26 Thioredoxin domain containing protein 4 precursor (Endoplasmic reticulum protein ERp44) 3 P09622 Dihydrolipoyl dehydrogenase, mitochondrial precursor (EC 1.8.1.4) (Dihydrolipoamide dehydro 3 P08708 40S ribosomal protein S17 3 Q96KP4 Cytosolic nonspecific dipeptidase (Glutamate carboxypeptidase-like protein 1) (CNDP dipepti 3 P14868 Aspartyl-tRNA synthetase (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS) 3 Q99497 DJ-1 protein (Oncogene DJ1) 3 Q12840 Neuronal kinesin heavy chain (NKHC) (Kinesin heavy chain isoform 5A) (Kinesin heavy chain ne 3 P00915 Carbonic anhydrase I (EC 4.2.1.1) (Carbonate dehydratase I) (CA-I) (Carbonic anhydrase B) 3 P20962 Parathymosin 3 Q99832 T-complex protein 1, eta subunit (TCP-1-eta) (CCT-eta) (HIV-1 Nef interacting protein) 3 Q15175 Paraneoplastic antigen (Fragment) 3 Q6UWP8 HLAR698 3 P20930 precursor (Fragment) 2 Q14789 Golgi autoantigen, golgin subfamily B member 1 (Giantin) (Macrogolgin) (Golgi complex-associa 2 P21728 D(1A) dopamine receptor 2 P17858 6-phosphofructokinase, liver type (EC 2.7.1.11) (Phosphofructokinase 1) (Phosphohexokinase) 2 Q9H223 EH-domain containing protein 4 (FKSG7 protein) (Hepatocellular carcinoma-associated prote 2 P43246 DNA mismatch repair protein Msh2 2 Q8N3H8 Hypothetical protein DKFZp761M1613 (Fragment) 2 Q8IYX7 Chromosome 9 open reading frame 138 2 Q8IV77 CNGA4 protein (Fragment) 2 O94842 Epidermal Langerhans cell protein LCP1 2 O75531 Barrier-to-autointegration factor (Breakpoint cluster region protein 1) 2 Q9UKJ8 ADAM 21 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 21) 2 O15269 Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (LCB 1) ( 2 P62195 26S protease regulatory subunit 8 (Proteasome subunit p45) (p45/SUG) (Proteasome 26S su 2 P61221 ATP-binding cassette sub-family E member 1 (RNase L inhibitor) (Ribonuclease 4 inhibitor) (R 2 P62269 40S ribosomal protein S18 (Ke-3) (Ke3) 2 P07305 Histone H1.0 (H1(0)) (Histone H1') 2 Q14697 Neutral alpha-glucosidase AB precursor (EC 3.2.1.84) (Glucosidase II alpha subunit) 2 Q04837 Single-stranded DNA-binding protein, mitochondrial precursor (Mt-SSB) (MtSSB) (PWP1-int 2 O95786 RNA helicase 2 P18615 Negative elongation factor E (NELF-E) (RD protein) 2 P18031 Tyrosine-protein phosphatase, non-receptor type 1 (EC 3.1.3.48) (Protein-tyrosine phosphata 2 O75460 Serine/threonine protein kinase/endoribonuclease IRE1 precursor (Inositol-requiring 1) (hIR 2 O60749 Sorting nexin 2 2 P09455 Retinol-binding protein I, cellular (Cellular retinol-binding protein) (CRBP) 2 O75074 Low-density lipoprotein receptor-related protein 3 precursor (hLRp105) 2 P35580 Myosin heavy chain, nonmuscle type B (Cellular myosin heavy chain, type B) (Nonmuscle myosi 2 P27105 Erythrocyte band 7 integral membrane protein (Stomatin) (Protein 7.2b) 2 P33527 Multidrug resistance-associated protein 1 (ATP-binding cassette, sub-family C, member 1) 2 Q96NL6 Hypothetical protein FLJ30655 2 Q9BSV6 tRNA-splicing endonuclease subunit SEN34 (EC 3.1.27.9) (tRNA-intron endonuclease SEN34 2 Q9Y4G6 2 2 Q9Y6V0 Piccolo protein (Aczonin) 2 Q9Y2B1 Transmembrane protein 5 2 Q9NYF0 Dapper homolog 1 (hDPR1) (Heptacellular carcinoma novel gene-3 protein) 2 Q6ZVZ3 Hypothetical protein FLJ41891 2 Q6ZSR4 Hypothetical protein FLJ45273 2 Q86TV6 Tetratricopeptide repeat protein 7B (Tetratricopeptide repeat protein 7 like-1) 2 Q6UXR7 LTLL9335 2 Q8TEG4 FLJ00233 protein (Fragment) 2 Q8TDY2 Rb1-inducible coiled coil protein 2 Q96BP3 KIAA0073 protein 2 Q96DB5 CGI-90 protein 2 Q8N531 F-box/LRR-repeat protein 6 (F-box and leucine-rich repeat protein 6) (F-box protein FBL6) 2 Supplemental Table 7: Proteins identified only in mid and poorly differentiated HNSCC

Peptides Accession Protein (number) P22695 Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) 6 P11047 Laminin gamma-1 chain precursor (Laminin B2 chain) 5 Q7Z5J4 Retinoic acid induced protein 1 4 Q9UKJ0 Activating receptor PILRbeta (Hypothetical protein DKFZp434O079) 4 Q9ULT2 KIAA1138 protein (Fragment) 4 Q6ZSN1 Hypothetical protein FLJ45355 4 O14686 Myeloid/lymphoid or mixed-lineage leukemia protein 2 (ALL1-related protein) 4 P15088 Mast cell carboxypeptidase A precursor (EC 3.4.17.1) (MC-CPA) (Carboxypeptidase A3) 3 O75694 Nuclear pore complex protein Nup155 (Nucleoporin Nup155) (155 kDa nucleoporin) 3 Q96LJ8 UBX domain-containing protein 3 3 P54577 Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS) 3 O75915 JWA protein (DERP11) (Dermal papilla derived protein 11) (Putative MAPK activating protein) (JM5 protein) 3 Q9H3N1 Thioredoxin domain containing protein 1 precursor (Transmembrane Trx-related protein) 3 Q96MC2 Hypothetical protein FLJ32660 3 Q6ZUF5 Hypothetical protein FLJ43756 3 P62241 40S ribosomal protein S8 2 P60228 Eukaryotic translation initiation factor 3 subunit 6 (eIF-3 p48) (eIF3e) (Viral integration site protein INT-6 ho 2 P62701 40S ribosomal protein S4, X isoform (Single copy abundant mRNA protein) (SCR10) 2 P50607 Tubby protein homolog 2 P49419 Aldehyde dehydrogenase family 7 member A1 (EC 1.2.1.3) (Antiquitin 1) 2 P14174 Macrophage migration inhibitory factor (MIF) (Phenylpyruvate tautomerase) (EC 5.3.2.1) 2 P00367 1, mitochondrial precursor (EC 1.4.1.3) (GDH) 2 P40763 Signal transducer and activator of transcription 3 (Acute-phase response factor) 2 O60674 Tyrosine-protein kinase JAK2 (EC 2.7.1.112) (Janus kinase 2) (JAK-2) 2 P42345 FKBP12-rapamycin complex-associated protein (FK506-binding protein 12-rapamycin complex-associated protein 2 P30520 Adenylosuccinate synthetase 2 (EC 6.3.4.4) (IMP--aspartate ligase 2) (AdSS 2) (AMPSase 2) 2 P31948 Stress-induced-phosphoprotein 1 (STI1) (Hsc70/Hsp90-organizing protein) (Hop) 2 Q9BW04 Specifically androgen-regulated protein (Hypothetical protein FLJ36507) 2 Q9ULX9 Transcription factor MafF (V- musculoaponeurotic fibrosarcoma oncogene homolog F) (U-Maf) 2 Q9UJ83 2-hydroxyphytanoyl-CoA (EC 4.1.-.-) (2-HPCL) (HSPC279) 2 Q16698 2,4-dienoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.34) (2,4-dienoyl-CoA reductase [NADPH]) 2 O00151 PDZ and LIM domain protein 1 (LIM domain protein CLP-36) (C-terminal LIM domain protein 1) (Elfin) 2 Q8WTS1 CGI58 protein 2 Q8TF30 KIAA1971 protein (Fragment) 2 Q8WWL7 G2/mitotic-specific cyclin B3 2 Q8NHS0 DnaJ homolog subfamily B member 8 2 Q8TD84 Down syndrome cell adhesion molecule 2 2 Q8TDM6 Discs, large homolog 5 (Placenta and prostate DLG) (Discs large protein P-dlg) 2 Q96BQ1 Protein FAM3D precursor (UNQ567/PRO1130) 2 Q92804 TATA-binding protein associated factor 2N (RNA-binding protein 56) (TAFII68) (TAF(II)68) 2 Supplemental Table 8: Classification-Biological Process

Biological Process Proteins Normal Well D Mod D Poorly D Cell Adhesion 134 25 42 39 28 Cell Cycle 153 16 49 45 43 Cell Differentiation 269 48 86 70 65 Cellular Metabolic Process 1153 174 352 306 321 Cell Motility 102 15 29 32 26 Endopeptidase Activity 53 7 14 17 15 Signal Transduction 371 53 125 101 92 Transcription 246 38 80 62 66 Translation 169 25 48 50 46 Supplemental Table 9: Proteins involved in signal transduction

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) P04083 Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobind 120 22 35 21 23 Q13835 Plakophilin 1 (Band-6-protein) (B6P) 95 17 31 21 32 P19971 precursor (EC 2040204) (TdRPase) ( 582503414 P61978 Heterogeneous nuclear ribonucleoprotein K (hnRNP K) (Transfo 48 10 29 27 33 P55072 Transitional endoplasmic reticulum ATPase (TER ATPase) (15S 373513214 P11021 78 kDa glucose-regulated protein precursor (GRP 78) (Immuno 36 3 47 28 22 P35579 Myosin heavy chain, nonmuscle type A (Cellular myosin heavy 36 3 42 31 25 P30101 Protein disulfide-isomerase A3 precursor (EC 5030401) (Disulfid 363363922 P06748 Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numat 21 14 29 14 43 P10599 Thioredoxin (ATL-derived factor) (ADF) (Surface associated sul 21 14 29 38 19 P22105 Tenascin X precursor (TN-X) (Hexabrachion-like) 17 0 41 29 29 P61604 10 kDa heat shock protein, mitochondrial (Hsp10) (10 kDa chap 14 29 0 0 71 P42224 Signal transducer and activator of transcription 1-alpha/beta (Tr 140572914 Q9P2E9 Ribosome-binding protein 1 (Ribosome receptor protein) (180 k 140433621 P46940 Ras GTPase-activating-like protein IQGAP1 (p195) 13 8 31 31 31 P06703 Calcyclin (Prolactin receptor associated protein) (PRA) (Growth 12 0 67 25 8 Q08881 Tyrosine-protein kinase ITK/TSK (EC 207010112) (T-cell-specif 11 18 36 27 18 P02675 Fibrinogen beta chain precursor [Contains: Fibrinopeptide B] 11 0 64 36 0 O75312 Zinc-finger protein ZPR1 (Zinc finger protein 259) 10 30 10 10 50 Q01518 Adenylyl cyclase-associated protein 1 (CAP 1) 10 10 30 20 40 P24821 Tenascin precursor (TN) (Hexabrachion) (Cytotactin) (Neuronec 10 0 60 40 0 P52565 Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha) 10 0 30 50 20 O00299 Chloride intracellular channel protein 1 (Nuclear chloride ion cha 911442222 P02671 Fibrinogen alpha/alpha-E chain precursor [Contains: Fibrinopep 8 0 63 38 0 Q9NZT1 Calmodulin-like protein 5 (Calmodulin-like skin protein) 8 0 50 25 25 P01024 Complement C3 precursor [Contains: C3a anaphylatoxin] 8 0 25 75 0 Q9UJU6 Drebrin-like protein (SH3 domain-containing protein 7) (Drebrin 7 14 57 29 0 P61088 Ubiquitin-conjugating enzyme E2 N (EC 60302019) (Ubiquitin-p 7 0 43 29 29 P14314 Glucosidase II beta subunit precursor (Protein kinase C substra 7 0 29 57 14 P27348 14-3-3 protein tau (14-3-3 protein theta) (14-3-3 protein T-cell) ( 7 0 29 43 29 P63000 Ras-related C3 botulinum toxin substrate 1 (p21-Rac1) (Ras-like 6670 0 33 Q96RJ0 Trace amine receptor 1 (TaR-1) 6 0 67 17 17 P61026 Ras-related protein Rab-10 6 0 50 17 33 Q9UBI6 Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-12 s 6 0 33 67 0 P62258 14-3-3 protein epsilon (14-3-3E) 6 0 17 67 17 P11233 Ras-related protein Ral-A 5 60 20 0 20 Q9NS15 Latent transforming growth factor beta binding protein 3 precurs 5 0 60 40 0 Q13442 28 kDa heat- and acid-stable phosphoprotein (PDGF-associated 5 0 40 40 20 Q8N442 Hypothetical protein FLJ13220 5 0 40 40 20 P35232 Prohibitin 5 0 20 20 60 P61981 14-3-3 protein gamma (Protein kinase C inhibitor protein-1) (KC 5 0 20 80 0 Q9Y3Z3 SAM domain and HD domain-containing protein 1 (Dendritic ce 5 0 0 100 0 Q92918 Mitogen-activated protein kinase kinase kinase kinase 1 (EC 20 4 75 0 25 0 Q99698 Lysosomal trafficking regulator (Beige homolog) 4 25 25 25 25 P21333 Filamin A (Alpha-filamin) (Filamin 1) (Endothelial actin-binding p 4 25 0 25 50 Q99665 Interleukin-12 receptor beta-2 chain precursor (IL-12 receptor b 4 25 0 50 25 O14745 Ezrin-radixin-moesin binding phosphoprotein 50 (EBP50) (Na(+ 4 0 75 0 25 P16144 Integrin beta-4 precursor (GP150) (CD104 antigen) 4 0 75 25 0 P00533 Epidermal growth factor receptor precursor (EC 207010112) (R 4 0 50 0 50 P51149 Ras-related protein Rab-7 4 0 50 0 50 P25103 Substance-P receptor (SPR) (NK-1 receptor) (NK-1R) (Tachykin 4 0 25 75 0 Q9UKJ0 Activating receptor PILRbeta (Hypothetical protein DKFZp434O 40 0 5050 P35813 Protein phosphatase 2C alpha isoform (EC 30103016) (PP2C-a 3 100 0 0 0 Q9Y561 Low-density lipoprotein receptor-related protein 12 precursor (S 3 100 0 0 0 P29373 Retinoic acid-binding protein II, cellular (CRABP-II) 3 67 0 0 33 P40145 Adenylate cyclase, type VIII (EC 4060101) (ATP pyrophosphate 3330 0 67 Q08380 Galectin-3 binding protein precursor (Lectin galactoside-binding 3 0 100 0 0 P40818 Ubiquitin carboxyl-terminal hydrolase 8 (EC 30102015) (Ubiquit 3 0 67 33 0 Q14573 Inositol 1,4,5-trisphosphate receptor type 3 (Type 3 inositol 1,4, 3 0 67 0 33 Q8WXD9 Cask-interacting protein 1 3 0 67 0 33 Q99497 DJ-1 protein (Oncogene DJ1) 3 0 67 33 0 Q9Y6E0 Serine/threonine-protein kinase 24 (EC 20701037) (STE20-like 3 0 67 0 33 O14511 Pro-neuregulin-2 precursor (Pro-NRG2) [Contains: Neuregulin-2 3 0 33 33 33 O43157 Plexin B1 precursor (Semaphorin receptor SEP) 3 0 33 33 33 P51148 Ras-related protein Rab-5C (RAB5L) (L1880) 3 0 33 0 67 Q7Z569 BRCA1-associated protein (EC 603020-) (BRAP2) (Impedes mi 3 0 33 0 67 Q9H3N1 Thioredoxin domain containing protein 1 precursor (Transmemb 30 0 6733 O94916 Nuclear factor of activated T cells 5 (T cell transcription factor N 2 100 0 0 0 P23458 Tyrosine-protein kinase JAK1 (EC 207010112) (Janus kinase 1 2 100 0 0 0 Q6UXX9 QFRL9384 2 100 0 0 0 O14727 Apoptotic protease activating factor 1 (Apaf-1) 2 50 50 0 0 P43405 Tyrosine-protein kinase SYK (EC 207010112) (Spleen tyrosine 2 50 50 0 0 Q13188 Serine/threonine-protein kinase 3 (EC 20701037) (STE20-like k 250500 0 P08173 Muscarinic acetylcholine receptor M4 2 50 0 50 0 Q15303 Receptor tyrosine-protein kinase erbB-4 precursor (EC 2070101 2500 0 50 Q99996 A-kinase anchor protein 9 (Protein kinase A anchoring protein 9 2500 0 50 P12429 Annexin A3 (Annexin III) (Lipocortin III) (Placental anticoagulant 2 0 100 0 0 P42261 Glutamate receptor 1 precursor (GluR-1) (GluR-A) (GluR-K1) (G 2 0 100 0 0 P62805 Histone H4 2 0 100 0 0 Q00587 CDC42 effector protein 1 (Serum protein MSE55) 2 0 100 0 0 Q15485 Ficolin 2 precursor (Collagen/fibrinogen domain-containing prote 2 0 100 0 0 Q8IW93 Rho guanine nucleotide exchange factor (GEF) 19 (Novel prote 2 0 100 0 0 Q96PE1 Probable G protein-coupled receptor 124 precursor (Tumor end 2 0 100 0 0 Q9NQS5 Inflammation-related G protein-coupled receptor EX33 (Putative 2 0 100 0 0 O75116 Rho-associated protein kinase 2 (EC 20701037) (Rho-associate 2 0 50 0 50 O75460 Serine/threonine protein kinase/endoribonuclease IRE1 precurs 2 0 50 50 0 P18031 Tyrosine-protein phosphatase, non-receptor type 1 (EC 301030 2 0 50 50 0 P21728 D(1A) dopamine receptor 2 0 50 50 0 Q9NYF0 Dapper homolog 1 (hDPR1) (Heptacellular carcinoma novel gen 2 0 50 50 0 O95661 Rho-related GTP-binding protein RhoI 2 0 0 100 0 Q01955 Collagen alpha 3(IV) chain precursor (Goodpasture antigen) 2 0 0 100 0 O60674 Tyrosine-protein kinase JAK2 (EC 207010112) (Janus kinase 2 2 0 0 50 50 P00367 Glutamate dehydrogenase 1, mitochondrial precursor (EC 1040 20 0 5050 P14174 Macrophage migration inhibitory factor (MIF) (Phenylpyruvate ta 20 0 5050 P40763 Signal transducer and activator of transcription 3 (Acute-phase 2 0 0 50 50 P42345 FKBP12-rapamycin complex-associated protein (FK506-binding 20 0 5050 Q8TDM6 Discs, large homolog 5 (Placenta and prostate DLG) (Discs larg 20 0 5050 Q96R06 Sperm associated antigen 5 (Astrin) (Mitotic spindle associated 2 0 0 0 100 Q9BZE4 Nucleolar GTP-binding protein 1 (Chronic renal failure gene pro 2000100 O15013 Rho guanine nucleotide exchange factor 10 1 100 0 0 0 P22455 Fibroblast growth factor receptor 4 precursor (EC 207010112) ( 1 100 0 0 0 P25054 Adenomatous polyposis coli protein (APC protein) 1 100 0 0 0 P43403 Tyrosine-protein kinase ZAP-70 (EC 207010112) (70 kDa zeta- 1 100 0 0 0 P48167 Glycine receptor beta chain precursor (Glycine receptor 58 kDa 1 100 0 0 0 P51813 Cytoplasmic tyrosine-protein kinase BMX (EC 207010112) (Bon 1 100 0 0 0 P78318 Immunoglobulin-binding protein 1 (CD79a-binding protein 1) (B 1 100 0 0 0 Q07001 Acetylcholine receptor protein, delta chain precursor 1 100 0 0 0 Q13445 Putative T1/ST2 receptor binding protein (Interleukin 1 receptor 1 100 0 0 0 Q8NGS5 Olfactory receptor 13C4 1 100 0 0 0 Q92914 Fibroblast growth factor-11 (FGF-11) (Fibroblast growth factor h 1 100 0 0 0 Q96RB7 Olfactory receptor 5M11 1 100 0 0 0 Q99704 Docking protein 1 (p62(dok)) (Downstream of tyrosine kinase 1) 1 100 0 0 0 Q9H4A3 Serine/threonine-protein kinase WNK1 (EC 20701037) (Protein 1 100 0 0 0 Q9UKU9 Angiopoietin-related protein 2 precursor (Angiopoietin-like 2) (U 1 100 0 0 0 Q9UQE7 Structural maintenance of chromosome 3 (Chondroitin sulfate p 1 100 0 0 0 Q9UQP3 Tenascin N precursor 1 100 0 0 0 O00230 Cortistatin precursor [Contains: Cortistatin-29; Cortistatin-17] 1 0 100 0 0 O00463 TNF receptor associated factor 5 (RING finger protein 84) 1 0 100 0 0 O00548 Delta-like protein 1 precursor (Drosophila Delta homolog 1) (De 1 0 100 0 0 O60237 Protein phosphatase 1 regulatory subunit 12B (Myosin phospha 1 0 100 0 0 O60266 Adenylate cyclase type III (EC 4060101) (Adenylate cyclase, olf 1 0 100 0 0 O95398 RAP guanine-nucleotide-exchange factor 3 (cAMP-regulated gu 1 0 100 0 0 P04114 Apolipoprotein B-100 precursor (Apo B-100) [Contains: Apolipo 1 0 100 0 0 P04150 Glucocorticoid receptor (GR) 1 0 100 0 0 P08069 Insulin-like growth factor I receptor precursor (EC 207010112) ( 1 0 100 0 0 P11487 INT-2 proto-oncogene protein precursor (Fibroblast growth facto 1 0 100 0 0 P23229 Integrin alpha-6 precursor (VLA-6) (CD49f) 1 0 100 0 0 P23468 Receptor-type tyrosine-protein phosphatase delta precursor (EC 1 0 100 0 0 P24046 Gamma-aminobutyric-acid receptor rho-1 subunit precursor (GA 1 0 100 0 0 P28907 ADP-ribosyl cyclase 1 (EC 3020205) (Cyclic ADP-ribose hydrola 1 0 100 0 0 P36405 ADP-ribosylation factor-like protein 3 1 0 100 0 0 P41236 Protein phosphatase inhibitor 2 (IPP-2) 1 0 100 0 0 P54762 Ephrin type-B receptor 1 precursor (EC 207010112) (Tyrosine-p 1 0 100 0 0 P55774 Small inducible cytokine A18 precursor (CCL18) (Macrophage i 1 0 100 0 0 P57075 UBASH3A protein 1 0 100 0 0 P59533 Taste receptor type 2 member 38 (T2R38) (T2R61) (PTC bitter 1 0 100 0 0 P59768 Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 su 1 0 100 0 0 P84095 Rho-related GTP-binding protein RhoG 1 0 100 0 0 Q06418 Tyrosine-protein kinase receptor TYRO3 precursor (EC 207010 1 0 100 0 0 Q07325 Small inducible cytokine B9 precursor (CXCL9) (Gamma interfe 1 0 100 0 0 Q13017 Rho-GTPase-activating protein 5 (p190-B) 1 0 100 0 0 Q13255 Metabotropic glutamate receptor 1 precursor (mGluR1) 1 0 100 0 0 Q16799 Reticulon 1 (Neuroendocrine-specific protein) 1 0 100 0 0 Q5U651 Ras-interacting protein 1 1 0 100 0 0 Q8IWN7 Retinitis pigmentosa 1-like 1 protein 1 0 100 0 0 Q8TAV4 Stomatin-like 3 1 0 100 0 0 Q8TDS5 G-protein coupled receptor TG1019 1 0 100 0 0 Q8WZA2 RAP guanine-nucleotide-exchange factor 4 (cAMP-regulated gu 1 0 100 0 0 Q92538 Golgi-specific brefeldin A-resistance guanine nucleotide exchan 1 0 100 0 0 Q92993 Histone acetyltransferase HTATIP (EC 20301048) (60 kDa Tat 1 0 100 0 0 Q93038 Tumor necrosis factor receptor superfamily member 25 precurs 1 0 100 0 0 Q96EY1 DnaJ homolog subfamily A member 3, mitochondrial precursor 1 0 100 0 0 Q96HE7 ERO1-like protein alpha precursor (EC 108040-) (ERO1-Lalpha 1 0 100 0 0 Q99572 P2X purinoceptor 7 (ATP receptor) (P2X7) (Purinergic receptor) 1 0 100 0 0 Q9BYZ6 Rho-related BTB domain-containing protein 2 (Deleted in breas 1 0 100 0 0 Q9H788 Hypothetical protein FLJ21146 1 0 100 0 0 Q9H9U2 Hypothetical protein FLJ12548 1 0 100 0 0 Q9NR61 Delta-like protein 4 precursor (Drosophila Delta homolog 4) (UN 1 0 100 0 0 Q9NRA0 Sphingosine kinase 2 (EC 207010-) (SK 2) (SPK 2) 1 0 100 0 0 Q9NRY4 Glucocorticoid receptor DNA binding factor 1 (Glucocorticoid rec 1 0 100 0 0 Q9NS28 Regulator of G-protein signaling 18 (RGS18) 1 0 100 0 0 Q9NVN3 Hypothetical protein FLJ10620 1 0 100 0 0 Q9NYY3 Serine/threonine-protein kinase PLK2 (EC 20701037) (Polo-like 1 0 100 0 0 Q9UHG0 Doublecortin domain-containing protein 2 (RU2S protein) 1 0 100 0 0 Q9UHI8 ADAMTS-1 precursor (EC 3040240-) (A disintegrin and metallo 1 0 100 0 0 Q9UHV7 -associated protein complex 240 kDa 1 0 100 0 0 Q9UKV3 Apoptotic chromatin condensation inducer in the nucleus (Acinu 1 0 100 0 0 Q9ULV8 Signal transduction protein CBL-C (SH3-binding protein CBL-C) 1 0 100 0 0 Q9UPU3 VPS10 domain-containing receptor SorCS3 precursor 1 0 100 0 0 Q9Y4H2 Insulin receptor substrate-2 (IRS-2) 1 0 100 0 0 O14907 Tax interaction protein 1 (Glutaminase-interacting protein 3) (Ta 1 0 0 100 0 O15263 Beta-defensin 2 precursor (BD-2) (hBD-2) (Defensin, beta 2) (S 1 0 0 100 0 O43182 Rho-GTPase-activating protein 6 (Rho-type GTPase-activating 1 0 0 100 0 O60229 Huntingtin-associated protein-interacting protein (Duo protein) 1 0 0 100 0 O60566 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta (E 1 0 0 100 0 O75912 Diacylglycerol kinase, iota (EC 207010107) (Diglyceride kinase) 1 0 0 100 0 O95672 Endothelin-converting enzyme-like 1 (EC 3040240-) (Xce protei 1 0 0 100 0 P01137 Transforming growth factor beta 1 precursor (TGF-beta 1) 1 0 0 100 0 P29218 Inositol-1(or 4)-monophosphatase (EC 30103025) (IMPase) (IM 1 0 0 100 0 P33241 Lymphocyte-specific protein 1 (Protein pp52) (52 kDa phosphop 1 0 0 100 0 P40616 ADP-ribosylation factor-like protein 1 1 0 0 100 0 P52566 Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (L 1 0 0 100 0 Q00013 55 kDa erythrocyte membrane protein (p55) (Membrane protein 1 0 0 100 0 Q01970 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase bet 1 0 0 100 0 Q13283 Ras-GTPase-activating protein binding protein 1 (GAP SH3-dom 1 0 0 100 0 Q13459 Myosin IXb (Unconventional myosin-9b) 1 0 0 100 0 Q14088 Ras-related protein Rab-33A (Small GTP-binding protein S10) 1 0 0 100 0 Q7Z727 Hypothetical protein (Fragment) 1 0 0 100 0 Q8NFN8 GABAB-related G-protein coupled receptor 1 0 0 100 0 Q92542 Nicastrin precursor (UNQ1874/PRO4317) 1 0 0 100 0 Q92772 P56 KKIAMRE protein kinase 1 0 0 100 0 Q93097 Wnt-2b protein precursor (Wnt-13) 1 0 0 100 0 Q99650 Oncostatin-M specific receptor beta subunit 1 0 0 100 0 Q9BPU6 Dihydropyrimidinase related protein-5 (DRP-5) (ULIP6 protein) 1 0 0 100 0 Q9C0C8 KIAA1735 protein (Fragment) 1 0 0 100 0 Q9GZM6 Olfactory receptor 8D2 (Olfactory receptor-like protein JCG2) 1 0 0 100 0 Q9H2E6 Semaphorin 6A precursor (Semaphorin VIA) (Sema VIA) (Sema 1 0 0 100 0 Q9HCU4 Cadherin EGF LAG seven-pass G-type receptor 2 precursor (E 1 0 0 100 0 Q9NP31 SH2 domain protein 2A (T cell-specific adapter protein) (TSAd) 1 0 0 100 0 Q9NP95 Fibroblast growth factor-20 (FGF-20) 1 0 0 100 0 Q9NYI0 Pleckstrin and Sec7 domain containing protein 3 (Exchange fac 1 0 0 100 0 Q9NYV9 Taste receptor type 2 member 13 (T2R13) (Taste receptor fami 1 0 0 100 0 Q9NZM3 Intersectin 2 (SH3 domain-containing protein 1B) (SH3P18) (SH 1 0 0 100 0 Q9UKE5 TRAF2 and NCK interacting kinase (EC 20701037) 1 0 0 100 0 Q9ULZ3 Apoptosis-associated speck-like protein containing a CARD (hA 1 0 0 100 0 Q9UQB3 Catenin delta-2 (Delta-catenin) (Neural plakophilin-related ARM 1 0 0 100 0 Q9Y3R0 Glutamate receptor-interacting protein 1 (GRIP1 protein) 1 0 0 100 0 O00366 Putative p150 1 0 0 0 100 O00560 Syntenin 1 (Syndecan binding protein 1) (Melanoma differentiat 1000100 O43396 Thioredoxin-like protein 1 (32 kDa thioredoxin-related protein) 1 0 0 0 100 P00797 Renin precursor (EC 304023015) (Angiotensinogenase) 1 0 0 0 100 P08648 Integrin alpha-5 precursor (Fibronectin receptor alpha subunit) ( 1000100 P11388 DNA topoisomerase II, alpha isozyme (EC 50990103) 1 0 0 0 100 P13521 Secretogranin II precursor (SgII) (Chromogranin C) [Contains: S 1000100 P20396 Thyroliberin precursor (Thyrotropin releasing hormone) (TRH) (T 1000100 P21796 Voltage-dependent anion-selective channel protein 1 (VDAC-1) 1 0 0 0 100 P25092 Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal gu 1000100 P35348 Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1 1000100 P40617 ADP-ribosylation factor-like protein 4A 1 0 0 0 100 P61106 Ras-related protein Rab-14 1 0 0 0 100 P62879 Guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 1 0 0 0 100 Q01484 Ankyrin 2 (Brain ankyrin) (Ankyrin B) (Ankyrin, nonerythroid) 1 0 0 0 100 Q15185 Telomerase-binding protein p23 (Hsp90 co-chaperone) (Proges 1000100 Q5VWB1 OTTHUMP00000059958 (Sorting nexin family member 27) 1 0 0 0 100 Q712M9 Serotonin receptor 5-HT4 1 0 0 0 100 Q8IUD2 ERC protein 1 (ELKS protein) 1 0 0 0 100 Q8NGV9 Seven transmembrane helix receptor 1 0 0 0 100 Q92572 Adapter-related protein complex 3 sigma 1 subunit (Sigma-adap 1000100 Q969V1 Melanin-concentrating hormone receptor 2 (MCH receptor 2) (M 1000100 Q9BUN8 Derlin-1 (Degradation in endoplasmic reticulum protein 1) (Der1 1 0 0 0 100 Q9BZ74 FKSG42 1 0 0 0 100 Q9H9L9 Hypothetical protein FLJ12664 1 0 0 0 100 Q9NP90 Ras-related protein Rab-9B (Rab-9L) (RAB9-like protein) 1 0 0 0 100 Q9NQT8 Kinesin-like protein KIF13B (Kinesin-like protein GAKIN) 1 0 0 0 100 Q9NTG1 Polycystic kidney disease and receptor for egg jelly related prot 1 0 0 0 100 Q9UL25 Ras-related protein Rab-21 1 0 0 0 100 Q9Y4F1 CDEP (FERM, RhoGEF, and pleckstrin domain protein 1, isofor 1000100 Q9Y4K4 Mitogen-activated protein kinase kinase kinase kinase 5 (EC 20 1000100 Supplemental Table 10: Proteins involved in protein phosphorylation

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) Q08881 Tyrosine-protein kinase ITK/TSK (EC 2.7.1.112) (T-cell-specific 11 18 36 27 18 P78527 DNA-dependent protein kinase catalytic subunit (EC 2.7.1.37) ( 9 11 0 22 67 O14757 Serine/threonine-protein kinase Chk1 (EC 2.7.1.37) 7 57 14 0 29 P20794 Serine/threonine-protein kinase MAK (EC 2.7.1.37) (Male germ 6 0 33 50 17 P00533 Epidermal growth factor receptor precursor (EC 2.7.1.112) (Rec 4 0 50 0 50 Q6P3R8 MGC75495 protein (OTTHUMP00000040896) 4 0 25 25 50 Q92918 Mitogen-activated protein kinase kinase kinase kinase 1 (EC 2.7 4 75 0 25 0 Q9Y6E0 Serine/threonine-protein kinase 24 (EC 2.7.1.37) (STE20-like ki 3 0 67 0 33 Q96Q04 KIAA1883 protein (Fragment) 3 33 33 0 33 O75116 Rho-associated protein kinase 2 (EC 2.7.1.37) (Rho-associated 2 0 50 0 50 O75460 Serine/threonine protein kinase/endoribonuclease IRE1 precurs 2 0 50 50 0 O60674 Tyrosine-protein kinase JAK2 (EC 2.7.1.112) (Janus kinase 2) ( 2 0 0 50 50 P43405 Tyrosine-protein kinase SYK (EC 2.7.1.112) (Spleen tyrosine ki 2 50 50 0 0 Q13188 Serine/threonine-protein kinase 3 (EC 2.7.1.37) (STE20-like kin 2 50 50 0 0 Q15303 Receptor tyrosine-protein kinase erbB-4 precursor (EC 2.7.1.11 2 50 0 0 50 Q96QT4 Transient receptor potential cation channel subfamily M membe 2500 050 P23458 Tyrosine-protein kinase JAK1 (EC 2.7.1.112) (Janus kinase 1) ( 2 100 0 0 0 P22455 Fibroblast growth factor receptor 4 precursor (EC 2.7.1.112) (FG 1 100 0 0 0 P43403 Tyrosine-protein kinase ZAP-70 (EC 2.7.1.112) (70 kDa zeta-as 1 100 0 0 0 P51813 Cytoplasmic tyrosine-protein kinase BMX (EC 2.7.1.112) (Bone 1 100 0 0 0 Q96RW7 Hemicentin 1 100 0 0 0 Q9H4A3 Serine/threonine-protein kinase WNK1 (EC 2.7.1.37) (Protein ki 1 100 0 0 0 P08069 Insulin-like growth factor I receptor precursor (EC 2.7.1.112) (C 1 0 100 0 0 P54762 Ephrin type-B receptor 1 precursor (EC 2.7.1.112) (Tyrosine-pro 1010000 Q06418 Tyrosine-protein kinase receptor TYRO3 precursor (EC 2.7.1.11 1010000 Q14766 Latent transforming growth factor beta binding protein, isoform 1 1010000 Q9NYY3 Serine/threonine-protein kinase PLK2 (EC 2.7.1.37) (Polo-like k 1010000 Q9Y6B5 PAK2 1 0 100 0 0 O00311 Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7-r 1 0 0 100 0 O60566 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta (E 1 0 0 100 0 P32780 TFIIH basal transcription factor complex p62 subunit (Basic tran 1 0 0 100 0 Q6P3W7 Similar to mouse D10Ertd802e protein 1 0 0 100 0 Q92772 P56 KKIAMRE protein kinase 1 0 0 100 0 Q9NZV1 Cysteine-rich repeat-containing protein S52 precursor (CRIM1) 1 0 0 100 0 Q9UKE5 TRAF2 and NCK interacting kinase (EC 2.7.1.37) 1 0 0 100 0 P25092 Heat-stable enterotoxin receptor precursor (GC-C) (Intestinal gu 1000100 Q86YV5 FLJ00269 protein (Fragment) 1000100 Q8IVW4 CDKL3 protein 1000100 Q9Y4K4 Mitogen-activated protein kinase kinase kinase kinase 5 (EC 2.7 1000100 Supplemental Table 11: Proteins involved in endopeptidase activity

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) P30101 Protein disulfide-isomerase A3 precursor (EC 5.3.4.1) (Disulfide 363363922 P28065 Proteasome subunit beta type 9 precursor (EC 3.4.25.1) (Protea 150474013 P07339 Cathepsin D precursor (EC 3.4.23.5) 13 0 62 23 15 P06733 Alpha enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyas 911223333 Q99797 Mitochondrial intermediate peptidase, mitochondrial precursor ( 6 0 50 17 33 P22695 Ubiquinol-cytochrome-c reductase complex core protein 2, mito 6 0 0 33 67 P25786 Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome co 3 0 67 33 0 P40818 Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin 3 0 67 33 0 P45974 Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin 3 0 0 100 0 P07384 Calpain 1, large [catalytic] subunit (EC 3.4.22.52) (Calcium-activ 250500 0 Q9UKJ8 ADAM 21 precursor (EC 3.4.24.-) (A disintegrin and metalloprot 2 0 50 50 0 P09936 Ubiquitin carboxyl-terminal hydrolase isozyme L1 (EC 3.4.19.12 2000100 Q96KR5 Leishmanolysin-like peptidase, variant 2 (EC 3.4.24.36) 2 0 0 100 0 O60235 Airway trypsin-like protease precursor (EC 3.4.21.-) 1 100 0 0 0 P13798 Acylamino-acid-releasing enzyme (EC 3.4.19.1) (AARE) (Acyl-p 1 100 0 0 0 Q9UBX1 Cathepsin F precursor (EC 3.4.22.41) (CATSF) 1 100 0 0 0 Q9UKR3 Kallikrein 13 precursor (EC 3.4.21.-) (Kallikrein-like protein 4) (K 1 100 0 0 0 O75173 ADAMTS-4 precursor (EC 3.4.24.82) (A disintegrin and metallo 1 0 100 0 0 P51784 Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquiti 1 0 100 0 0 P78562 Phosphate regulating neutral endopeptidase (EC 3.4.24.-) (Meta 1010000 Q9P2N4 ADAMTS-9 precursor (EC 3.4.24.-) (A disintegrin and metallopr 1010000 Q9UHI8 ADAMTS-1 precursor (EC 3.4.24.-) (A disintegrin and metallopr 1010000 O95672 Endothelin-converting enzyme-like 1 (EC 3.4.24.-) (Xce protein) 1 0 0 100 0 P07711 Cathepsin L precursor (EC 3.4.22.15) (Major excreted protein) ( 1 0 0 100 0 P20618 Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome com 1 0 0 100 0 Q6MZZ7 Hypothetical protein DKFZp686L13193 1 0 0 100 0 Q9NZV1 Cysteine-rich repeat-containing protein S52 precursor (CRIM1) 1 0 0 100 0 Q9ULZ3 Apoptosis-associated speck-like protein containing a CARD (hA 1 0 0 100 0 O43464 Serine protease HTRA2, mitochondrial precursor (EC 3.4.21.-) 1000100 P00797 Renin precursor (EC 3.4.23.15) (Angiotensinogenase) 1000100 P04632 Calpain small subunit 1 (CSS1) (Calcium-dependent protease s 1000100 P17538 Chymotrypsinogen B precursor (EC 3.4.21.1) 1000100 P49720 Proteasome subunit beta type 3 (EC 3.4.25.1) (Proteasome the 1000100 P60900 Proteasome subunit alpha type 6 (EC 3.4.25.1) (Proteasome iot 1000100 Q8NBP7 Proprotein convertase subtilisin/kexin type 9 precursor (EC 3.4. 1000100 Q8TE58 ADAMTS-15 precursor (EC 3.4.24.-) (A disintegrin and metallop 1000100 Supplemental Table 12: Proteins involved in cell motility

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) P04083 Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobind 120 22 35 21 23 P04792 Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) 835293135 P08670 Vimentin 79 0 37 44 19 P35579 Myosin heavy chain, nonmuscle type A (Cellular myosin heavy 36 3 42 31 25 P61160 Actin-like protein 2 (Actin-related protein 2) 26 8 38 31 23 P67936 alpha 4 chain (Tropomyosin 4) (TM30p1) 22 0 41 32 27 P10599 Thioredoxin (ATL-derived factor) (ADF) (Surface associated sul 21 14 29 38 19 P18206 (Metavinculin) 18 11 50 28 11 O43707 Alpha-actinin 4 (Non-muscle alpha-actinin 4) (F-actin cross linki 16 0 44 19 38 P26038 Moesin (Membrane-organizing extension spike protein) 15 0 13 60 27 P31146 Coronin-1A (Coronin-like protein p57) (Coronin-like protein A) (C 110274527 Q01518 Adenylyl cyclase-associated protein 1 (CAP 1) 10 10 30 20 40 P52565 Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha) 10 0 30 50 20 P05023 Sodium/potassium-transporting ATPase alpha-1 chain precurso 7 0 29 43 29 P63000 Ras-related C3 botulinum toxin substrate 1 (p21-Rac1) (Ras-like 6670 033 P12814 Alpha-actinin 1 (Alpha-actinin cytoskeletal isoform) (Non-muscle 6 0 83 0 17 P25815 S-100P protein 5 0 80 20 0 P52907 F-actin capping protein alpha-1 subunit (CapZ alpha-1) 4 25 25 25 25 P21333 Filamin A (Alpha-filamin) (Filamin 1) (Endothelial actin-binding p 4 25 0 25 50 P00533 Epidermal growth factor receptor precursor (EC 2.7.1.112) (Rec 4 0 50 0 50 P29034 S100 calcium-binding protein A2 (S-100L protein) (CAN19) 3 0 67 33 0 O43157 Plexin B1 precursor (Semaphorin receptor SEP) 3 0 33 33 33 P54577 Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tR 3 0 0 33 67 P07942 Laminin beta-1 chain precursor (Laminin B1 chain) 2 50 50 0 0 P43405 Tyrosine-protein kinase SYK (EC 2.7.1.112) (Spleen tyrosine ki 2 50 50 0 0 Q8TE73 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chai 2 50 50 0 0 P35580 Myosin heavy chain, nonmuscle type B (Cellular myosin heavy 2 0 50 50 0 P43246 DNA mismatch repair protein Msh2 2 0 50 50 0 O60674 Tyrosine-protein kinase JAK2 (EC 2.7.1.112) (Janus kinase 2) ( 2 0 0 50 50 P40763 Signal transducer and activator of transcription 3 (Acute-phase 2 0 0 50 50 Q13591 Semaphorin 5A precursor (Semaphorin F) (Sema F) 1 100 0 0 0 Q9UQP3 Tenascin N precursor 1 100 0 0 0 O14556 Glyceraldehyde-3-phosphate dehydrogenase, testis-specific (EC 1010000 O15143 ARP2/3 complex 41 kDa subunit (P41-ARC) (Actin-related prote 1010000 P23229 Integrin alpha-6 precursor (VLA-6) (CD49f) 1 0 100 0 0 Q9UHG0 Doublecortin domain-containing protein 2 (RU2S protein) 1 0 100 0 0 P01137 Transforming growth factor beta 1 precursor (TGF-beta 1) 1 0 0 100 0 P13637 Sodium/potassium-transporting ATPase alpha-3 chain (EC 3.6.3 1 0 0 100 0 P29966 Myristoylated alanine-rich C-kinase substrate (MARCKS) (Prote 1 0 0 100 0 P33241 Lymphocyte-specific protein 1 (Protein pp52) (52 kDa phosphop 1 0 0 100 0 P36952 Maspin precursor (Protease inhibitor 5) 1 0 0 100 0 P52566 Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (L 1 0 0 100 0 Q9BPU6 Dihydropyrimidinase related protein-5 (DRP-5) (ULIP6 protein) 1 0 0 100 0 Q9H2E6 Semaphorin 6A precursor (Semaphorin VIA) (Sema VIA) (Sema 1 0 0 100 0 O00560 Syntenin 1 (Syndecan binding protein 1) (Melanoma differentiat 1000100 P13521 Secretogranin II precursor (SgII) (Chromogranin C) [Contains: S 1000100 Q02880 DNA topoisomerase II, beta isozyme (EC 5.99.1.3) 1000100 Supplemental Table 13: Proteins involved in cell cycle regulation

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) P04083 Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobind 120 22 35 21 23 P06748 Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Numat 21 14 29 14 43 O43707 Alpha-actinin 4 (Non-muscle alpha-actinin 4) (F-actin cross linki 16 0 44 19 38 P42224 Signal transducer and activator of transcription 1-alpha/beta (Tr 140572914 P78371 T-complex protein 1, beta subunit (TCP-1-beta) (CCT-beta) 13 15 31 31 23 P06703 Calcyclin (Prolactin receptor associated protein) (PRA) (Growth 12 0 67 25 8 P31146 Coronin-1A (Coronin-like protein p57) (Coronin-like protein A) (C 110274527 Q9BPX3 Condensin subunit 3 (Chromosome-associated protein G) (Con 10 0 50 20 30 P27797 Calreticulin precursor (CRP55) (Calregulin) (HACBP) (ERp60) ( 8 0 50 13 38 O14757 Serine/threonine-protein kinase Chk1 (EC 2.7.1.37) 7 57 14 0 29 P27348 14-3-3 protein tau (14-3-3 protein theta) (14-3-3 protein T-cell) ( 7 0 29 43 29 Q16543 Hsp90 co-chaperone Cdc37 (Hsp90 chaperone protein kinase-t 6 0 67 0 33 Q13561 Dynactin complex 50 kDa subunit (50 kDa dynein-associated po 5010000 P50991 T-complex protein 1, delta subunit (TCP-1-delta) (CCT-delta) (S 5 0 40 60 0 P35232 Prohibitin 5 0 20 20 60 O60231 Putative pre-mRNA splicing factor RNA helicase (ATP-depende 425252525 P00533 Epidermal growth factor receptor precursor (EC 2.7.1.112) (Rec 4 0 50 0 50 Q13148 TAR DNA-binding protein-43 (TDP-43) 4 0 50 25 25 Q9UHD8 Septin 9 (MLL septin-like fusion protein) (MLL septin-like fusion 4 0 50 25 25 P07954 Fumarate hydratase, mitochondrial precursor (EC 4.2.1.2) (Fum 3330 067 P20962 Parathymosin 3 0 67 33 0 Q99832 T-complex protein 1, eta subunit (TCP-1-eta) (CCT-eta) (HIV-1 3 0 67 33 0 Q02224 Centromeric protein E (CENP-E protein) 3 0 33 33 33 Q9HC35 Echinoderm microtubule-associated protein-like 4 (EMAP-4) (Re 250500 0 P46087 Proliferating-cell nucleolar antigen (Proliferation-associate 2500 050 Q14526 Hypermethylated in cancer 1 protein (Hic-1) (Zinc finger and BT 2500 050 O60447 EVI-5 homolog 2 0 100 0 0 P52292 Importin alpha-2 subunit (Karyopherin alpha-2 subunit) (SRP1-a 2010000 O75460 Serine/threonine protein kinase/endoribonuclease IRE1 precurs 2 0 50 50 0 P43246 DNA mismatch repair protein Msh2 2 0 50 50 0 Q14566 DNA replication licensing factor MCM6 (P105MCM) 2 0 50 0 50 Q8TDY2 Rb1-inducible coiled coil protein 2 0 50 50 0 O60674 Tyrosine-protein kinase JAK2 (EC 2.7.1.112) (Janus kinase 2) ( 2 0 0 50 50 O95661 Rho-related GTP-binding protein RhoI 2 0 0 100 0 P33992 DNA replication licensing factor MCM5 (CDC46 homolog) (P1-C 2000100 P42345 FKBP12-rapamycin complex-associated protein (FK506-binding 2 0 0 50 50 P49736 DNA replication licensing factor MCM2 (Minichromosome maint 2000100 P62701 40S ribosomal protein S4, X isoform (Single copy abundant mR 2 0 0 50 50 Q8TDM6 Discs, large homolog 5 (Placenta and prostate DLG) (Discs larg 2 0 0 50 50 Q8WWL7 G2/mitotic-specific cyclin B3 2 0 0 50 50 Q96R06 Sperm associated antigen 5 (Astrin) (Mitotic spindle associated 2000100 Q9Y265 RuvB-like 1 (EC 3.6.1.-) (49-kDa TATA box-binding protein-inte 2 0 0 100 0 O75122 KIAA0627 protein (Fragment) 1 100 0 0 0 O75909 Cyclin K 1 100 0 0 0 P25054 Adenomatous polyposis coli protein (APC protein) 1 100 0 0 0 Q14674 Separin (EC 3.4.22.49) (Separase) (Caspase-like protein ESPL 1 100 0 0 0 Q16164 G1 phase-specific gene protein (Fragment) 1 100 0 0 0 Q96HI0 Sentrin-specific protease 5 (EC 3.4.22.-) (Sentrin/SUMO-specifi 1 100 0 0 0 Q9UQE7 Structural maintenance of chromosome 3 (Chondroitin sulfate p 1 100 0 0 0 O15287 Fanconi anemia group G protein (FACG protein) (DNA-repair pr 1010000 O43303 Centrosomal protein of 110 kDa (CP110 protein) 1 0 100 0 0 O43663 Protein regulating cytokinesis 1 (Protein regulator of cytokinesis 1010000 O60884 DnaJ homolog subfamily A member 2 (HIRA interacting protein 1 0 100 0 0 P06454 Prothymosin alpha 1 0 100 0 0 P08069 Insulin-like growth factor I receptor precursor (EC 2.7.1.112) (C 1 0 100 0 0 P11487 INT-2 proto-oncogene protein precursor (Fibroblast growth facto 1010000 P28340 DNA polymerase delta catalytic subunit (EC 2.7.7.7) (DNA poly 1 0 100 0 0 P42695 Hypothetical protein KIAA0056 (Fragment) 1 0 100 0 0 P50748 Kinetochore-associated protein 1 (Rough deal homolog) (hRod) 1010000 P78344 Eukaryotic translation initiation factor 4 gamma 2 (eIF-4-gamma 1010000 P84095 Rho-related GTP-binding protein RhoG 1 0 100 0 0 Q01831 DNA-repair protein complementing XP-C cells (Xeroderma pigm 1010000 Q13618 Cullin homolog 3 (CUL-3) 1 0 100 0 0 Q6KC79 Nipped-B-like protein (Delangin) (SCC2 homolog) 1 0 100 0 0 Q8TEW8 Amyotrophic lateral sclerosis 2 chromosome region candidate g 1010000 Q8WTW4 Tumor suppressor candidate 4 (NPR2-like) (Gene 21 protein) (G 1010000 Q9NRY4 Glucocorticoid receptor DNA binding factor 1 (Glucocorticoid rec 1010000 Q9NYY3 Serine/threonine-protein kinase PLK2 (EC 2.7.1.37) (Polo-like k 1010000 Q9UQL6 (HD5) (Antigen NY-CO-9) 1 0 100 0 0 O00311 Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7-r 1 0 0 100 0 O60566 Mitotic checkpoint serine/threonine-protein kinase BUB1 beta (E 1 0 0 100 0 P01137 Transforming growth factor beta 1 precursor (TGF-beta 1) 1 0 0 100 0 P27694 Replication protein A 70 kDa DNA-binding subunit (RP-A) (RF-A 1 0 0 100 0 P30622 Restin (Cytoplasmic linker protein-170 alpha-2) (CLIP-170) (Ree 1 0 0 100 0 P32780 TFIIH basal transcription factor complex p62 subunit (Basic tran 1 0 0 100 0 P49646 Very very hypothetical protein RMSA-1 1 0 0 100 0 P52789 Hexokinase, type II (EC 2.7.1.1) (HK II) (Muscle form hexokinas 1 0 0 100 0 Q96EP1 Ubiquitin ligase protein CHFR (EC 6.3.2.-) (Checkpoint with fork 1 0 0 100 0 Q99496 DinG protein (Ring finger protein BAP-1) (Ring finger protein 2) 1 0 0 100 0 Q9H5I1 Histone-lysine N-methyltransferase, H3 lysine-9 specific 2 (EC 2 1 0 0 100 0 Q9NQW6 Actin binding protein anillin 1 0 0 100 0 Q9NY59 Neutral sphingomyelinase II (EC 3.1.4.12) 1 0 0 100 0 Q9ULZ3 Apoptosis-associated speck-like protein containing a CARD (hA 1 0 0 100 0 Q9UQ80 Proliferation-associated protein 2G4 (Cell cycle protein p38-2G4 1 0 0 100 0 Q9Y250 Leucine zipper putative tumor suppressor 1 (F37/esophageal ca 1 0 0 100 0 Q9Y3P9 Rab6 GTPase activating protein, GAPCenA (RABGAP1 protein 1 0 0 100 0 O00366 Putative p150 1000100 O43324 Multisynthetase complex auxiliary component p18 1000100 P25205 DNA replication licensing factor MCM3 (DNA polymerase alpha 1000100 P33993 DNA replication licensing factor MCM7 (CDC47 homolog) (P1.1 1000100 P51610 Host cell factor C1 (HCF) (VP16 accessory protein) (HFC1) (VC 1000100 P55769 NHP2-like protein 1 (High mobility group-like nuclear protein 2 h 1000100 Q00577 Transcriptional activator protein PUR-alpha (Purine-rich single-s 1000100 Q12959 Presynaptic protein SAP97 (Synapse-associated protein 97) (D 1000100 Q92900 Regulator of nonsense transcripts 1 (Nonsense mRNA reducing 1000100 Q99460 26S proteasome non-ATPase regulatory subunit 1 (26S proteas 1000100 Q99684 Zinc finger protein Gfi-1 (Growth factor independence-1) 1000100 Q9BTV7 Cdk5 and abl enzyme substrate 2 (Interactor with cdk3 2) (Ik3-2 1000100 Q9UBU7 Activator of S phase Kinase (Dbf4 protein) 1000100 Supplemental Table 14: Proteins involved in cell adhesion

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) Q13835 Plakophilin 1 (Band-6-protein) (B6P) 95 17 31 21 32 P12111 Collagen alpha 3(VI) chain precursor 69 3 32 46 19 P32926 Desmoglein 3 precursor (130 kDa pemphigus vulgaris antigen) 65 15 29 31 25 P35579 Myosin heavy chain, nonmuscle type A (Cellular myosin heavy 36 3 42 31 25 Q9Y446 Plakophilin 3 35 29 29 31 11 P07737 Profilin-1 (Profilin I) 24 17 21 29 33 P47929 Galectin-7 (Gal-7) (HKL-14) (PI7) (p53-induced protein 1) 24 8 67 13 13 Q8NFW1 Alpha 1 type XXII collagen 22 0 32 41 27 Q14574 Desmocollin 3 precursor (Desmocollin 4) (HT-CP) 18 17 22 22 39 P18206 Vinculin (Metavinculin) 18 11 50 28 11 P22105 Tenascin X precursor (TN-X) (Hexabrachion-like) 17 0 41 29 29 Q02413 Desmoglein 1 precursor (Desmosomal glycoprotein 1) (DG1) (D 14 14 36 43 7 Q13753 Laminin gamma-2 chain precursor (Kalinin/nicein/epiligrin 100 k 13 0 62 38 0 P24821 Tenascin precursor (TN) (Hexabrachion) (Cytotactin) (Neuronec 10 0 60 40 0 P20908 Collagen alpha 1(V) chain precursor 10 0 50 30 20 P52565 Rho GDP-dissociation inhibitor 1 (Rho GDI 1) (Rho-GDI alpha) 10 0 30 50 20 Q02388 Collagen alpha 1(VII) chain precursor (Long-chain collagen) (LC 922111156 Q13751 Laminin beta-3 chain precursor (Laminin 5 beta 3) (Laminin B1k 9 0 44 56 0 Q02487 Desmocollin 2A/2B precursor (Desmosomal glycoprotein II and 7 0 43 29 29 P63000 Ras-related C3 botulinum toxin substrate 1 (p21-Rac1) (Ras-like 6670 033 Q8N8Z6 Discoidin, CUB and LCCL domain containing protein 1 precurso 61733500 P12814 Alpha-actinin 1 (Alpha-actinin cytoskeletal isoform) (Non-muscle 6 0 83 0 17 P16615 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6 5 0 40 60 0 P11047 Laminin gamma-1 chain precursor (Laminin B2 chain) 5 0 0 60 40 P16144 Integrin beta-4 precursor (GP150) (CD104 antigen) 4 0 75 25 0 P00533 Epidermal growth factor receptor precursor (EC 2.7.1.112) (Rec 4 0 50 0 50 Q08380 Galectin-3 binding protein precursor (Lectin galactoside-binding 3010000 P13611 Versican core protein precursor (Large fibroblast proteoglycan) 2 100 0 0 0 O14727 Apoptotic protease activating factor 1 (Apaf-1) 2 50 50 0 0 P07942 Laminin beta-1 chain precursor (Laminin B1 chain) 2 50 50 0 0 P43405 Tyrosine-protein kinase SYK (EC 2.7.1.112) (Spleen tyrosine ki 2 50 50 0 0 Q96QT4 Transient receptor potential cation channel subfamily M membe 2500 050 Q15582 Transforming growth factor-beta induced protein IG-H3 precurso 2010000 Q8TEG4 FLJ00233 protein (Fragment) 2 0 50 50 0 Q99715 Collagen alpha 1(XII) chain precursor 2 0 50 0 50 Q9Y4G6 Talin 2 2 0 50 50 0 Q01955 Collagen alpha 3(IV) chain precursor (Goodpasture antigen) 2 0 0 100 0 Q8TD84 Down syndrome cell adhesion molecule 2 2 0 0 50 50 Q8TDM6 Discs, large homolog 5 (Placenta and prostate DLG) (Discs larg 2 0 0 50 50 Q96KR5 Leishmanolysin-like peptidase, variant 2 (EC 3.4.24.36) 2 0 0 100 0 O15537 Retinoschisin precursor (X-linked juvenile retinoschisis protein) 1 100 0 0 0 P25054 Adenomatous polyposis coli protein (APC protein) 1 100 0 0 0 Q13591 Semaphorin 5A precursor (Semaphorin F) (Sema F) 1 100 0 0 0 Q86XX4 Extracellular matrix protein FRAS1 precursor 1 100 0 0 0 Q96RW7 Hemicentin 1 100 0 0 0 Q9UN73 Protocadherin alpha 6 precursor (PCDH-alpha6) 1 100 0 0 0 Q9UQP3 Tenascin N precursor 1 100 0 0 0 O00548 Delta-like protein 1 precursor (Drosophila Delta homolog 1) (De 1010000 P01042 Kininogen precursor (Alpha-2-thiol proteinase inhibitor) [Contain 1010000 P20849 Collagen alpha 1(IX) chain precursor 1 0 100 0 0 P23229 Integrin alpha-6 precursor (VLA-6) (CD49f) 1 0 100 0 0 P35609 Alpha-actinin 2 (Alpha actinin skeletal muscle isoform 2) (F-acti 1 0 100 0 0 Q06418 Tyrosine-protein kinase receptor TYRO3 precursor (EC 2.7.1.11 1010000 Q13017 Rho-GTPase-activating protein 5 (p190-B) 1 0 100 0 0 Q8TDX9 Polycystic kidney disease 1-like 1 protein (Polycystin 1L1) 1 0 100 0 0 Q9H251 Cadherin-23 precursor (Otocadherin) 1 0 100 0 0 Q9NRY4 Glucocorticoid receptor DNA binding factor 1 (Glucocorticoid rec 1010000 O43182 Rho-GTPase-activating protein 6 (Rho-type GTPase-activating 1 0 0 100 0 P04275 Von Willebrand factor precursor (vWF) [Contains: Von Willebran 1 0 0 100 0 P13942 Collagen alpha 2(XI) chain precursor 1 0 0 100 0 P22223 Cadherin-3 precursor (Placental-cadherin) (P-cadherin) 1 0 0 100 0 P52566 Rho GDP-dissociation inhibitor 2 (Rho GDI 2) (Rho-GDI beta) (L 1 0 0 100 0 Q86SJ2 Amphoterin induced gene 2 (DEGA/AMIGO-2 precursor) (Alivin 1 0 0 100 0 Q9HCU4 Cadherin EGF LAG seven-pass G-type receptor 2 precursor (E 1 0 0 100 0 Q9UQB3 Catenin delta-2 (Delta-catenin) (Neural plakophilin-related ARM 1 0 0 100 0 Q9Y5G7 Protocadherin gamma A6 precursor (PCDH-gamma-A6) 1 0 0 100 0 Q9Y6C2 EMILIN 1 precursor (Elastin microfibril interface-located protein 1 0 0 100 0 P08648 Integrin alpha-5 precursor (Fibronectin receptor alpha subunit) ( 1000100 Q12959 Presynaptic protein SAP97 (Synapse-associated protein 97) (D 1000100 Q86UX7 Unc-112 related protein 2 (Kindlin-3) (MIG2-like) 1000100 Q9NY15 Stabilin 1 precursor (FEEL-1 protein) (MS-1 antigen) 1000100 Supplemental Table 15: Novel proteins identified in HNSCC

Peptides Normal Well D Mod D Poorly D Accession Protein (number) (%) (%) (%) (%) Q8N7Z2 Hypothetical protein FLJ40198 15 0.00 40.00 33.33 26.67 Q9BVC6 Hypothetical protein MGC5508 13 0.00 23.08 30.77 46.15 Q96MG1 Hypothetical protein FLJ32421 10 10.00 50.00 30.00 10.00 Q96CN5 Hypothetical protein MGC20806 10 30.00 40.00 10.00 20.00 Q6ZT17 Hypothetical protein FLJ45043 8 12.50 25.00 25.00 37.50 Q6ZVY6 Hypothetical protein FLJ41910 8 0.00 0.00 0.00 100.00 Q6ZRH9 Hypothetical protein FLJ46347 7 0.00 42.86 42.86 14.29 Q96LT0 Hypothetical protein FLJ25091 7 0.00 57.14 14.29 28.57 Q6ZQN2 Hypothetical protein FLJ46846 7 0.00 42.90 57.10 0.00 Q66K23 Hypothetical protein (Fragment) 7 0.00 42.90 57.10 0.00 Q8N7I6 Hypothetical protein FLJ25506 6 16.67 16.67 33.33 33.33 Q6ZVR1 Hypothetical protein FLJ42200 6 0.00 16.67 66.67 16.67 Q5VVY7 OTTHUMP00000040479 6 0.00 50.00 33.33 16.67 Q13015 Protein AF1q 6 0.00 0.00 0.00 100.00 Q6IQ21 Hypothetical protein FLJ20582 5 0.00 40.00 40.00 20.00 Q8N442 Hypothetical protein FLJ13220 5 0.00 40.00 40.00 20.00 Q6ZRU0 Hypothetical protein FLJ46111 5 0.00 42.90 57.10 0.00 Q8TBU6 Hypothetical protein FLJ11848 4 25.00 25.00 25.00 25.00 Q9H8N1 Hypothetical protein FLJ13385 4 0.00 25.00 25.00 50.00 Q6P3R8 MGC75495 protein (OTTHUMP00000040896) 4 0.00 25.00 25.00 50.00 Q96FV1 KRT19 protein (Fragment) 4 0.00 0.00 0.00 100.00 Q9Y6X9 LOC132200 protein 4 0.00 0.00 0.00 100.00 Q8N9V6 Hypothetical protein FLJ36160 4 0.00 60.00 40.00 0.00 Q9H7V7 Hypothetical protein FLJ14207 4 0.00 50.00 50.00 0.00 Q86T83 Hypothetical protein DKFZp451J0218 4 0.00 66.70 33.30 0.00 Q9ULT2 KIAA1138 protein (Fragment) 4 0.00 0.00 50.00 50.00 Q6ZSN1 Hypothetical protein FLJ45355 4 0.00 0.00 75.00 25.00 Q9BZK3 FKSG17 3 0.00 33.33 33.33 33.33 Q96NZ8 Putative multivalent protease inhibitor WFIKKN 3 0.00 33.33 33.33 33.33 Q6ZN03 Hypothetical protein FLJ16545 3 100.00 0.00 0.00 0.00 Q9HCF8 KIAA1614 protein (Fragment) 3 0.00 100.00 0.00 0.00 Q6NXN2 Hypothetical protein 3 0.00 66.70 33.30 0.00 Q86Z22 Hypothetical protein 3 0.00 33.30 66.70 0.00 Q6UWP8 HLAR698 3 0.00 66.70 33.30 0.00 Q96MC2 Hypothetical protein FLJ32660 3 0.00 0.00 75.00 25.00 Q6ZUF5 Hypothetical protein FLJ43756 3 0.00 0.00 50.00 50.00 Q9H0M3 Hypothetical protein DKFZp434O0710 (Hypothetical protein KIA 2 100.00 0.00 0.00 0.00 Q9UGU5 High-mobility group protein 2-like 1 (HMGBCG protein) 2 100.00 0.00 0.00 0.00 Q6ZWK7 Hypothetical protein FLJ16045 2 100.00 0.00 0.00 0.00 Q7Z7J3 Hypothetical protein 2 100.00 0.00 0.00 0.00 Q6UXX9 QFRL9384 2 100.00 0.00 0.00 0.00 Q96PE1 Probable G protein-coupled receptor 124 precursor (Tumor end 2 0.00 100.00 0.00 0.00 O15074 KIAA0368 protein (Fragment) 2 0.00 100.00 0.00 0.00 Q9H7W7 Hypothetical protein FLJ14183 2 0.00 100.00 0.00 0.00 Q6ZNX0 Hypothetical protein FLJ26965 2 0.00 100.00 0.00 0.00 Q63HQ8 Hypothetical protein DKFZp686M21196 2 0.00 100.00 0.00 0.00 Q8IYW7 Hypothetical protein (Fragment) 2 0.00 100.00 0.00 0.00 Q8IW93 Rho guanine nucleotide exchange factor (GEF) 19 (Novel prote 2 0.00 100.00 0.00 0.00 Q8N9S5 Hypothetical protein FLJ36608 2 0.00 100.00 0.00 0.00 O15032 KIAA0316 protein (Fragment) 2 0.00 0.00 100.00 0.00 Q9BU70 Chromosome 9 open reading frame 156 2 0.00 0.00 100.00 0.00 Q9NWL6 Hypothetical protein FLJ20752 (HCV NS3-transactivated protein 2 0.00 0.00 100.00 0.00 Q6ZRD7 Hypothetical protein FLJ46433 2 0.00 0.00 100.00 0.00 Q8TE28 BA351K23.4 (Novel protein) (Hypothetical protein FLJ25831) 2 0.00 0.00 100.00 0.00 Q8IYW2 Chromosome 10 open reading frame 92 2 0.00 0.00 100.00 0.00 Q8N7E2 Hypothetical protein FLJ25735 2 0.00 0.00 100.00 0.00 Q9H977 Hypothetical protein FLJ12953 2 0.00 0.00 0.00 100.00 P30740 Hypothetical protein FLJ42406 2 50.00 50.00 0.00 0.00 Q8N3H8 Hypothetical protein DKFZp761M1613 (Fragment) 2 0.00 50.00 50.00 0.00 Q8IYX7 Chromosome 9 open reading frame 138 2 0.00 50.00 50.00 0.00 Q8IV77 CNGA4 protein (Fragment) 2 0.00 50.00 50.00 0.00 Q96NL6 Hypothetical protein FLJ30655 2 0.00 50.00 50.00 0.00 Q6ZVZ3 Hypothetical protein FLJ41891 2 0.00 50.00 50.00 0.00 Q6ZSR4 Hypothetical protein FLJ45273 2 0.00 50.00 50.00 0.00 Q6UXR7 LTLL9335 2 0.00 50.00 50.00 0.00 Q8TEG4 FLJ00233 protein (Fragment) 2 0.00 50.00 50.00 0.00 Q96BP3 KIAA0073 protein 2 0.00 50.00 50.00 0.00 Q96DB5 CGI-90 protein 2 0.00 50.00 50.00 0.00 Q8WTS1 CGI58 protein 2 0.00 0.00 50.00 50.00 Q8TF30 KIAA1971 protein (Fragment) 2 0.00 0.00 50.00 50.00

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