Supporting Information for Proteomics DOI 10.1002/pmic.200500052

Yurong Guo, Shwu-Fan Ma, Dmitry Grigoryev, Jennifer Van Eyk and Joe G. N. Garcia

1-DE MS and 2-D LC-MS analysis of the mouse bronchoalveolar lavage proteome

ª 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Supplemetary table 1. List of proteins involved in biological process based on gene ontology analysis using GeneMapp [30] and Mappfinder [31]. complement activation\, alternative pathway Complement component C9 precursor Properdin (Factor P) hemolytic complement histocompatibility 2, complement component factor B; Factor B adipsin; D component (adipsin) of complement Complement C3 precursor (HSE-MSF) complement activation Complement component C9 precursor Properdin (Factor P) complement component 4 (within H-2S) hemolytic complement RIKEN cDNA 1700013L23 histocompatibility 2, complement component factor B; Factor B adipsin; D component (adipsin) of complement Complement factor I precursor (C3B/C4B inactivator) acute-phase response Alpha-1-antitrypsin 1-2 precursor coagulation factor II; prothrombin Fibronectin precursor (FN) hemopexin regenerating islet-derived 3 gamma serine (or cysteine) proteinase inhibitor, clade A, member 1d serine (or cysteine) proteinase inhibitor, clade A, member 1e serine (or cysteine) proteinase inhibitor, clade F, member 2 glycolysis Dihydrolipoyl dehydrogenase, mitochondrial precursor Glyceraldehyde 3-phosphate dehydrogenase glyceraldehyde-3-phosphate dehydrogenase lactate dehydrogenase 2, B chain; phosphoglycerate kinase 1 pyruvate kinase liver and red blood cell Pyruvate kinase, M2 isozyme triosephosphate isomerase response to oxidative stress Glutathione peroxidase isocitrate dehydrogenase 1 (NADP+), soluble peroxiredoxin 1; proliferation-associated gene A Peroxiredoxin 2 (Thioredoxin peroxidase 1) Plasma glutathione peroxidase precursor superoxide dismutase 1, soluble; Cu(2+)-Zn2+ sup Supplementary table 1 continued. blood coagulation annexin A5; annexin V coagulation factor II; prothrombin Kininogen precursor [Contains: Bradykinin] serine (or cysteine) proteinase inhibitor, clade C (antithrombin) serine (or cysteine) proteinase inhibitor, clade D, member 1 carbohydrate metabolism Alpha-amylase, salivary and hepatic precursor Chitinase-3 like protein 1 precursor Dihydrolipoyl dehydrogenase, mitochondrial precursor Glyceraldehyde 3-phosphate dehydrogenase glyceraldehyde-3-phosphate dehydrogenase Isocitrate dehydrogenase isocitrate dehydrogenase 1 (NADP+), soluble lactate dehydrogenase 2, B chain; lysozyme Malate dehydrogenase, cytoplasmic malic enzyme, supernatant P lysozyme structural phosphoglycerate kinase 1 putative chitinase precursor; chitinase, acidic pyruvate kinase liver and red blood cell Pyruvate kinase, M2 isozyme transaldolase 1 triosephosphate isomerase inflammatory response CD14 antigen Complement C3 precursor (HSE-MSF) hemolytic complement Kininogen precursor [Contains: Bradykinin] regenerating islet-derived 3 gamma toll-like receptor 5 proteolysis and peptidolysis a disintegrin and metalloprotease domain 7 adipsin; D component (adipsin) of complement cathepsin B preproprotein cathepsin D cathepsin H; Cat H Cathepsin S precursor Cathepsin Z precursor coagulation factor II; prothrombin Complement factor I precursor (C3B/C4B inactivator) Dipeptidyl-peptidase I precursor (DPP-I) (DPPI) dipeptidylpeptidase III glutamyl aminopeptidase Supplementary table 1 continued. proteolysis and peptidolysis histocompatibility 2, complement component factor B; Factor B kidney-derived aspartic protease-like protein prolyl endopeptidase; prolyl oligopeptidase Prostasin precursor (Channel activating protease 1) Protein-glutamine gamma-glutamyltransferase Serine protease hepsin cell adhesion catenin alpha 1; alpha E catenin; alpha(E)-catenin Fibronectin precursor (FN) fibulin 5 intercellular adhesion molecule Junction plakoglobin (Desmoplakin III) laminin, gamma 1; laminin B2 neuropilin; Neuropilin-1 plakophilin 1 Platelet glycoprotein IV Pulmonary surfactant-associated protein A precursor Supplementary table 2. Comparison of the results of mouse BALF proteins identified from this study with rat BALF proteins identified from 2D gel [14]. Only unique proteins are listed, and immunoglobulin isoforms are not listed here. rat BALF proteins identified corresponding mouse proteins identified corresponding mouse proteins identified from 2D gel from 1D PAGE followed by LC MS/MS by 2D LC MS/MS Afamin Yes Yes Albumin Yes Yes α-1 major acute phase protein No No α-1-Antitrypsin Yes Yes α-1-inhibitor III No No α-2 HS-glycoprotein (fetuin) Yes Yes β-1-globin No No β-globin No No Apolipoprotein A-IV Yes Yes c-active protein No No Calgranulin A (fragment) No No Calgranulin B No No Complement component 3 Yes Yes Contrapsin-like protease inhibitor 1 No No Contrapsin-like protease inhibitor 3 No No Contrapsin-like protease inhibitor 6 No No Ferroxidase No No Fetuin β Yes Yes Fibrinogen β-chain No No Haptoglobin Yes Yes Hemoglobin α-chain Yes Yes Hemoglobin β-chain Yes Yes Hemopexin Yes Yes inter-α-inhibitor H4 heavy chain No No Lipocortin 1 Yes Yes Serotransferrin No No Serum amyloid P-component No No Thioredoxin peroxidase 1 Yes Yes T-kininogen Yes Yes T-kininogen II No No Transthyretin Yes Yes Vitamin D binding protein Yes Yes Supplementary table 3. Comparison of the results of mouse BALF proteins identified from this study with human BALF proteins identified from 2D gel [8,12]. Only unique proteins are listed, and immunoglobulin isoforms are not listed here. Human BALF proteins identified corresponding mouse proteins identified corresponding mouse proteins identified from 2D gel from 1D PAGE followed by LC MS/MS by 2D LC MS/MS Actin β chain Yes Yes Actin γ chain No No Acyl coA binding protein like No No Albumin Yes Yes Aldehyde reductase Yes Yes Aldehyde dehydrogenase I Yes Yes Antioxidant protein II Yes Yes α-1 Antichymotrypsin Yes Yes α-1 Antiprotease No No α-1 Antitrypsin Yes Yes α-1 β glycoprotein No No α-1 Microglobulin No No α-2 Antiplasmin No No α2-HS-glycoprotein Yes Yes α2-Macroglobulin Yes Yes Amyloid P No No Antioxidant enzyme Yes Yes Antithrombin III chain A Yes Yes Apolipoprotein D No No Apolipoprotein A1 Yes Yes Apolipoprotein A II Yes Yes Apolipoprotein A IV Yes Yes β 2 Microglobulin No No β-galactosidase binding lectin No No Calcyclin (S100A6 protein) No No Calcyphosine No No Calgizzarin (S100c protein) No No Calgranulin A No No Calgranulin C No No Calreticulin No No Calvasculin (S100A4 protein) No No Cathepsin D No Yes Cathepsin H No Yes Ceruloplasmin Yes Yes Clara cell protein 16 No No Clusterin No No Complement C3 Yes Yes Complement factor 4γ No Yes Complement factor B Yes Yes Cystatin S No No Epididymal secretory protein No No Fatty acid-binding protein, adipocyte No No Fatty acid-binding protein, epidermal No No Fibrinogen β-chain No No Fibrinogen γ-chain No No Glutathione S transferase, chain A Yes Yes Supplementary table 3 continued. Human BALF proteins identified corresponding mouse proteins identified corresponding mouse proteins identified from 2D gel from 1D PAGE followed by LC MS/MS by 2D LC MS/MS GTP cyclohydrolase I feedback No No regulatory protein Haptoglobin-1 (α1-chain) Yes Yes Haptoglobin-2 (α2-chain) Yes Yes Haptoglobin-2 (β2-chain) Yes Yes Heat shock cognate 70 kDa Yes Yes Hemoglobin α chain Yes Yes Hemoglobin β chain Yes Yes Hemopexin Yes Yes Immunoglobulin binding factor No No Intestinal trefoil factor No No Lactoferrin Yes Yes Leucine-rich α2-glycoprotein No No Lipocalin 1 No No Lipocortin 1 Yes Yes Lysozyme C Yes Yes Macrophage colony stimulating factor 1NoNo MHC class II antigen DRB3 No No Monocyte neutrophil elastase inhibitor No No Nuclear chloride ion channel 27 No No Orosomucoid No No Peptidyl-prolyl cis-trans isomerase A No Yes Peptidyl-prolyl cis-trans isomerase B No No Peripheral blood leukocytes peptide 474aa No No Phosphatidylthanolamine binding protein Yes Yes Plasma retinol-binding protein No No Plasminogen Yes Yes L-Plastin Yes Yes Prothrombin Yes Yes Retinol binding protein Yes No Rho GDP dissociation inhibitor α Yes Yes Saposin D-chain No No SH3 domain binding glutamic No No acid-rich protein like Superoxide dismutase (Cu/Zn) No Yes Superoxide dismutase (Mn) Yes No Surfactant protein A Yes Yes Thioredoxin No Yes Transferrin Yes Yes Transthyretin No Yes Triosephosphate isomerase Yes Yes Tropomyosin α-chain skeletal muscle type Yes Yes Tubulin β2NoYes Ubiquitin Yes No unknown protein (homology to coactosin) No No Supplementary table 3 continued. Human BALF proteins identified corresponding mouse proteins identified corresponding mouse proteins identified from 2D gel from 1D PAGE followed by LC MS/MS by 2D LC MS/MS Vimentin (fragment) No No Vitamin D binding protein Yes Yes Zinc α2-glycoprotein Yes Yes