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Electronic Supplementary Material (ESI) for Metallomics This journal is © The Royal Society of Chemistry 2013 1 Supporting Figure Legend 2 3 Figure S1: RPS4Y1 mRNA levels. Levels of this mRNA were measured as part of the validation of Affymetrix gene expression data from DEG.C. Cclones are controls (untreated 4 Beas-2B that grew in soft agar) and Vclones are clones transformed by chronic NaVO3 exposure. 5 6 Figure S1 7 8 9 Table S1: Differentially expressed genes in transformed clones (DEG.C). Gene Symbol Gene Description Adjusted Fold p-value change TMEM47 transmembrane protein 47 1.9E-02 36.196 SPTLC3 serine palmitoyltransferase, long chain base subunit 3 7.8E-03 33.565 RPS4Y1 ribosomal protein S4, Y-linked 1 6.9E-03 28.724 EYA4 eyes absent homolog 4 (Drosophila) 3.9E-03 18.298 EIF1AY eukaryotic translation initiation factor 1A, Y-linked 8.6E-03 13.872 EDIL3 EGF-like repeats and discoidin I-like domains 3 1.3E-02 12.147 DDX3Y DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, Y-linked 3.9E-03 12.110 UTY ubiquitously transcribed tetratricopeptide repeat gene, Y-linked 9.5E-03 10.134 CYP1B1 cytochrome P450, family 1, subfamily B, polypeptide 1 2.2E-02 9.194 CD24 CD24 molecule 1.4E-02 8.328 1 Electronic Supplementary Material (ESI) for Metallomics This journal is © The Royal Society of Chemistry 2013 GABRA3 gamma-aminobutyric acid (GABA) A receptor, alpha 3 1.7E-02 7.643 ZNF730 zinc finger protein 730 2.0E-02 7.283 RARB|LOC100130354 retinoic acid receptor, beta | hypothetical protein LOC100130354 3.3E-02 7.168 DNER delta/notch-like EGF repeat containing 3.6E-02 7.067 SERPINB2|SERPINB10 serpin peptidase inhibitor, clade B (ovalbumin), member 2 | serpin peptidase inhibitor, clade B (ovalbumin), 1.6E-02 6.863 member 10 USP9Y ubiquitin specific peptidase 9, Y-linked 7.8E-03 6.194 PPAPDC1A phosphatidic acid phosphatase type 2 domain containing 1A 1.6E-02 5.853 HLF hepatic leukemia factor 4.3E-02 5.837 ASAM adipocyte-specific adhesion molecule 2.0E-02 5.425 ABI3BP ABI family, member 3 (NESH) binding protein 4.5E-02 5.381 ZFY zinc finger protein, Y-linked 1.8E-02 5.288 NTN4 netrin 4 2.2E-02 5.284 ZNF300 zinc finger protein 300 1.4E-02 4.987 WNT5A wingless-type MMTV integration site family, member 5A 1.7E-02 4.967 COL5A2 collagen, type V, alpha 2 2.1E-02 4.931 MGAM maltase-glucoamylase (alpha-glucosidase) 3.1E-02 4.716 ZNF280B zinc finger protein 280B 2.1E-02 4.649 F2RL2 coagulation factor II (thrombin) receptor-like 2 2.9E-02 4.600 SRPX2 sushi-repeat-containing protein, X-linked 2 9.9E-03 4.590 PDE1C phosphodiesterase 1C, calmodulin-dependent 70kDa 1.4E-02 4.495 PRICKLE1 prickle homolog 1 (Drosophila) 3.4E-02 4.390 CYorf15A chromosome Y open reading frame 15A 1.5E-02 4.302 LGR4 leucine-rich repeat-containing G protein-coupled receptor 4 1.1E-02 4.015 GLIS3 GLIS family zinc finger 3 1.1E-02 3.998 NRP1 neuropilin 1 1.9E-02 3.990 IL31RA interleukin 31 receptor A 3.6E-02 3.907 CRISPLD2 cysteine-rich secretory protein LCCL domain containing 2 3.6E-02 3.815 SLC4A4 solute carrier family 4, sodium bicarbonate cotransporter, member 4 1.9E-02 3.793 SNAI2 snail homolog 2 (Drosophila) 1.8E-02 3.733 MEIS1 Meis homeobox 1 1.3E-02 3.720 2 Electronic Supplementary Material (ESI) for Metallomics This journal is © The Royal Society of Chemistry 2013 SPOCK1 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1 2.4E-02 3.654 MMP16 matrix metallopeptidase 16 (membrane-inserted) 1.8E-02 3.643 TGFA transforming growth factor, alpha 2.3E-02 3.607 ZNF717|LOC100287163 zinc finger protein 717 | similar to Zinc finger protein 717 7.8E-03 3.590 TNC tenascin C 8.0E-03 3.522 FHDC1 FH2 domain containing 1 1.1E-02 3.496 PPP1R3C protein phosphatase 1, regulatory (inhibitor) subunit 3C 1.9E-02 3.474 SNORD13 small nucleolar RNA, C/D box 13 2.5E-02 3.348 ADAM12 ADAM metallopeptidase domain 12 3.4E-02 3.324 LOC554202 microRNA 31 1.5E-02 3.317 NTF3 neurotrophin 3 3.4E-02 3.314 NEGR1 neuronal growth regulator 1 3.6E-02 3.312 SNORD13|RNU13P3 small nucleolar RNA, C/D box 13 | RNA, U13 small nuclear pseudogene 3 2.5E-02 3.303 SH3RF2 SH3 domain containing ring finger 2 1.8E-02 3.296 MPP4 membrane protein, palmitoylated 4 (MAGUK p55 subfamily member 4) 1.7E-02 3.168 SLC8A1 solute carrier family 8 (sodium/calcium exchanger), member 1 3.3E-02 3.157 CD109 CD109 molecule 3.8E-02 3.131 KDM5D lysine (K)-specific demethylase 5D 7.8E-03 3.108 MAMLD1 mastermind-like domain containing 1 8.6E-03 3.059 DUSP4 dual specificity phosphatase 4 1.5E-02 3.043 TES testis derived transcript (3 LIM domains) 1.8E-02 3.022 SLC16A2 solute carrier family 16, member 2 (monocarboxylic acid transporter 8) 8.1E-03 2.976 G0S2 G0/G1switch 2 3.6E-02 2.952 PRICKLE2 prickle homolog 2 (Drosophila) 1.7E-02 2.951 GLT8D4 glycosyltransferase 8 domain containing 4 1.1E-02 2.919 KIAA1217 sickle tail protein homolog 2.2E-02 2.855 MST131 MSTP131 2.1E-02 2.854 SYTL2 synaptotagmin-like 2 2.0E-02 2.833 SHISA2 shisa homolog 2 (Xenopus laevis) 2.1E-02 2.822 KCTD4 potassium channel tetramerisation domain containing 4 3.6E-03 2.771 ITGBL1 integrin, beta-like 1 (with EGF-like repeat domains) 2.4E-03 2.697 3 Electronic Supplementary Material (ESI) for Metallomics This journal is © The Royal Society of Chemistry 2013 GPR39|LYPD1 G protein-coupled receptor 39 | LY6/PLAUR domain containing 1 3.1E-02 2.664 ARRDC3 arrestin domain containing 3 2.2E-02 2.654 LAMB3 laminin, beta 3 2.8E-02 2.641 CHST11 carbohydrate (chondroitin 4) sulfotransferase 11 3.7E-02 2.618 FOXD1 forkhead box D1 1.0E-02 2.604 PTPRS protein tyrosine phosphatase, receptor type, S 4.4E-02 2.555 GPR56 G protein-coupled receptor 56 2.3E-02 2.551 SATB2 SATB homeobox 2 3.0E-02 2.548 TOX2 TOX high mobility group box family member 2 1.5E-02 2.531 EMP1 epithelial membrane protein 1 2.4E-02 2.525 BACE1 beta-site APP-cleaving enzyme 1 4.9E-02 2.521 CORO2B coronin, actin binding protein, 2B 2.3E-02 2.491 MID1 midline 1 (Opitz/BBB syndrome) 1.5E-02 2.484 PTGER2 prostaglandin E receptor 2 (subtype EP2), 53kDa 2.3E-02 2.483 ANTXR2 anthrax toxin receptor 2 1.3E-02 2.459 OPN3|KMO opsin 3 | kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) 8.6E-03 2.442 ABLIM3 actin binding LIM protein family, member 3 2.7E-02 2.435 INPP4B inositol polyphosphate-4-phosphatase, type II, 105kDa 4.7E-02 2.434 LRIG1 leucine-rich repeats and immunoglobulin-like domains 1 2.6E-02 2.426 ZNF608 zinc finger protein 608 2.3E-02 2.388 C5orf13 chromosome 5 open reading frame 13 1.9E-02 2.374 HPCAL1 hippocalcin-like 1 2.0E-02 2.352 CYorf15B chromosome Y open reading frame 15B 4.1E-02 2.350 TGFBR2 transforming growth factor, beta receptor II (70/80kDa) 1.2E-02 2.331 CDH4 cadherin 4, type 1, R-cadherin (retinal) 3.6E-02 2.331 NRIP1 nuclear receptor interacting protein 1 1.8E-02 2.322 PER3|UTS2 period homolog 3 (Drosophila) | urotensin 2 1.5E-02 2.317 FAM172A family with sequence similarity 172, member A 3.3E-02 2.309 TUBA1A tubulin, alpha 1a 3.4E-02 2.266 LY6K lymphocyte antigen 6 complex, locus K 2.5E-02 2.231 PNPLA3 patatin-like phospholipase domain containing 3 2.7E-02 2.219 4 Electronic Supplementary Material (ESI) for Metallomics This journal is © The Royal Society of Chemistry 2013 SEMA7A semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group) 3.7E-02 2.209 ATL1 atlastin GTPase 1 2.6E-02 2.209 ITFG1 integrin alpha FG-GAP repeat containing 1 2.0E-02 2.204 MARVELD2 MARVEL domain containing 2 4.4E-02 2.203 HOXB2 homeobox B2 2.4E-02 2.203 JAG1 jagged 1 (Alagille syndrome) 8.1E-03 2.197 MARVELD2 MARVEL domain containing 2 4.5E-02 2.196 MMP14 matrix metallopeptidase 14 (membrane-inserted) 4.5E-02 2.173 STC2 stanniocalcin 2 2.6E-02 2.168 PIK3R3 phosphoinositide-3-kinase, regulatory subunit 3 (gamma) 1.5E-02 2.167 SPOCD1 SPOC domain containing 1 2.0E-02 2.165 ATG10 autophagy related 10 2.7E-02 2.149 NRG1 neuregulin 1 3.1E-02 2.144 S1PR1 sphingosine-1-phosphate receptor 1 1.5E-02 2.140 PRKY protein kinase, Y-linked 8.0E-03 2.113 LAMB1 laminin, beta 1 3.2E-02 2.111 AOX1 aldehyde oxidase 1 8.6E-03 2.099 SERPINE2 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 4.3E-02 2.093 PLCE1 phospholipase C, epsilon 1 4.4E-02 2.093 CUZD1 CUB and zona pellucida-like domains 1 2.8E-02 2.086 FN1 fibronectin 1 2.0E-02 2.083 ITGA5 integrin, alpha 5 (fibronectin receptor, alpha polypeptide) 1.1E-02 2.083 DYSF dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive) 4.1E-02 2.061 ADA adenosine deaminase 2.2E-02 2.052 VDR vitamin D (1,25- dihydroxyvitamin D3) receptor 1.4E-02 2.047 SLC6A8|SLC6A10P solute carrier family 6 (neurotransmitter transporter, creatine), member 8 | solute carrier family 6 2.0E-02 2.043 (neurotransmitter transporter, creatine), member 10 (pseudogene) GDF15 growth differentiation factor 15 4.9E-02 2.040 ECM1 extracellular matrix protein 1 1.6E-02 2.034 LHFPL2 lipoma HMGIC fusion partner-like 2 4.3E-02 2.027 CPEB2 cytoplasmic polyadenylation element binding protein 2 2.7E-02 2.025 5 Electronic Supplementary Material (ESI) for Metallomics This journal is © The Royal Society of Chemistry 2013 TMEM14A transmembrane protein 14A 1.7E-02 2.024 HOMER2 homer homolog 2 (Drosophila) 4.0E-02 2.022 PHLDA1 pleckstrin homology-like domain, family A, member 1 4.8E-02 2.017 TSPAN15 tetraspanin 15 2.4E-02 2.014 ARHGAP18 Rho GTPase activating protein 18 4.8E-02 2.014 SLC6A8|SLC6A10P solute carrier family 6 (neurotransmitter transporter, creatine), member 8 | solute carrier family 6 2.2E-02 2.004 (neurotransmitter transporter, creatine), member 10 (pseudogene) LRP1 low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) 1.8E-02 1.999
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  • The Plasma Peptides of Alzheimer's Disease

    The Plasma Peptides of Alzheimer's Disease

    Florentinus‑Mefailoski et al. Clin Proteom (2021) 18:17 https://doi.org/10.1186/s12014‑021‑09320‑2 Clinical Proteomics RESEARCH Open Access The plasma peptides of Alzheimer’s disease Angelique Florentinus‑Mefailoski1, Peter Bowden1, Philip Scheltens2, Joep Killestein3, Charlotte Teunissen4 and John G. Marshall1,5* Abstract Background: A practical strategy to discover proteins specifc to Alzheimer’s dementia (AD) may be to compare the plasma peptides and proteins from patients with dementia to normal controls and patients with neurological condi‑ tions like multiple sclerosis or other diseases. The aim was a proof of principle for a method to discover proteins and/ or peptides of plasma that show greater observation frequency and/or precursor intensity in AD. The endogenous tryptic peptides of Alzheimer’s were compared to normals, multiple sclerosis, ovarian cancer, breast cancer, female normal, sepsis, ICU Control, heart attack, along with their institution‑matched controls, and normal samples collected directly onto ice. Methods: Endogenous tryptic peptides were extracted from blinded, individual AD and control EDTA plasma sam‑ ples in a step gradient of acetonitrile for random and independent sampling by LC–ESI–MS/MS with a set of robust and sensitive linear quadrupole ion traps. The MS/MS spectra were ft to fully tryptic peptides within proteins identi‑ fed using the X!TANDEM algorithm. Observation frequency of the identifed proteins was counted using SEQUEST algorithm. The proteins with apparently increased observation frequency in AD versus AD Control were revealed graphically and subsequently tested by Chi Square analysis. The proteins specifc to AD plasma by Chi Square with FDR correction were analyzed by the STRING algorithm.