Table I Proteome profile of low abundance protein sera fractions in human patients with cardiomyopathy of chagasic and other etiologies

Human sera samples were depleted of high abundance proteins using IgY-12 high capacity LC10 proteome partitioning chromatography. The enriched, low abundance proteins were resolved by the ProteomeLab PF-2D approach, and protein fractions eluted after second dimension high performance reverse phase chromatography were collected in 96-well plates. Proteins fractions/protein peaks uniquely detected in sera samples from normal healthy subjects with no disease, cardiomyopathy patients of other etiologies and chagasic patients were subjected to MALDI-TOF MS/MS analysis, and proteins identified by homology search against Swiss-prot database. The putative biological function and cellular location were identified using ingenuity pathway analysis and the UniProt system. The selected, differentially expressed protein fractions were resolved by SDS-PAGE and subjected to Western blotting with anti-DNPH antibody to detect DNPH-derivatized carbonyl post-translational modification. The extent of carbonylation is recorded as − (absent) or +, ++, and +++ when <25%, 25–50%, and >50% of the expressed protein was modified. NA, information not available in public databases.

Gene nameProtein nameSwiss-Prot GI numberProtein molecular mass (kDa)Protein score (%)Protein pICarbonylationBiological/molecular functionCellular location
Protein peaks specific to normal subjects with no disease (i.e., down-regulated in chagasic subjects)
    APOC3Apolipoprotein C-III11402610,8461005.23Lipid transportExtracellular
    ATG16L1Autophagy protein 16-L16251048268,22390.836.2Protein transportCytoplasm
    C4BPAC4b-binding protein α41673366,9891007.15Innate responseExtracellular
    CLPBCaseinolytic peptidase B2500926778,68094.969.13Heat responseNA
    CLUClusterin11653352,4611005.89Anti-apoptoticExtracellular
    DPP10Dipeptidyl peptidase 105762890,87681.706.11ProteolysisMembrane
    EEA1Early endosome antigen 1229462866162,36788.725.55EndosomalMembrane
    F2Prothrombin13580769,9921005.64Acute phase responseExtracellular
    IGHA1Immunoglobulin heavy α-111358437,6311006.08Immune responseExtracellular
    IGHA2Immunoglobulin heavy α-221851208836,5031005.71Immune responseMembrane
    KIAA1210Uncharacterized protein262527575186,90589.948.72NANA
    KRT2Keratin, type II cytoskeletal 223993865065,39393.368.07Epidermis developIntermediate filament
    MYH14Myosin heavy chain 1471151982227,86397.175.76Cell shapeMyosin complex
    PRLProlactin13093025,85978.996.5Cell proliferationExtracellular
    SPATA1Spermatogenesis-associated protein 120583005850,27692.018.54NANA
    TTRTransthyretin13646415,87787.045.52TransportExtracellular
Protein peaks specific to patients with cardiomyopathy of other etiologies
    AMBPα-1-Microglobulin12280138,974715.95Host-pathogenExtracellular
    C4BComplement C4-B81175167192,6732866.73InflammatoryExtracellular
    CKAP2LCytoskeleton assoc protein 222447189183,46683.699.82NANA
    COL21A1Collagen type XXI α-17475207199,30788.458.57Cell adhesionCytoplasm
    GPLD1Glycan-sp phospholipase D12630258392,2781805.91Protein releaseSecreted
    HIST1H2BHistone cluster 1H2B type 146223613,94215810.31Nucleosome assemblyNucleus
    ITIH2Inter-α trypsin inhibitor H2229462889106,3975116.4Hyaluronan metabolismExtracellular
    KNG1Kininogen 112405647471,9121046.34VasodilationExtracellular
    PCID2PCI domain-protein 28568103446,00079.478.78NANA
    SERPING1Serpin peptidase inhibitor G112409655,1191716.09Innate immune responseExtracellular
    SUCLG2Succinyl-CoA ligase 25278829246,48160.876.15Carbohydrate metabolismMitochondria
    TTLL8Tubulin tyrosine ligase-like 819041098790,69897.908.48Protein polyglycylationCytoplasm
    VCLVinculin21903479123,72279.55.5Muscle contractionExtracellular
Protein peaks specific to patients with cardiomyopathy of chagasic origin
    BCL2A1Bcl-2-related protein A1249328020,11964.315.33+++Anti-apoptoticCytoplasm
    C14ORF57Uncharacterized protein7115204514,66486.749.34NANA
    C4BPAC4b-binding protein α41673366,9891007.15+++Innate immune responseExtracellular
    C9orf135Uncharacterized protein7474698726,42887.636.75NAMembrane
    CASP10Caspase-101264446358,91389.226.95+++ApoptosisNA
    CFBComplement factor B58490885,47999.956.67Complement activationExtracellular
    CPCeruloplasmin116117122,1281005.44Oxidation reductionExtracellular
    CTTNCortactin16869362961,54959.035.24NACytoplasm
    DAPL1Death-associated protein-like 116701206011,87375.8710ApoptosisNA
    DCPSScavenger mRNA-decapper11624132538,58583.695.93mRNA catabolismNucleus
    DIP2ADisco-interacting protein 2A32700084170,26176.428.35Catalytic activityNucleus
    DNAH17Dynein heavy chain 17172044714511,46094.725.56Microtubule movementCytoplasm
    F13BCoagulation factor XIII B14555947375,46199.256.01Blood coagulationExtracellular
    CCNB1G2/mitotic-specific cyclin-B111617648,30672.937.09Cell cycleSpindle pole
    GCVitamin D-binding protein13964152,9291005.4TransportExtracellular
    GCNT1Glucosaminyl (N-acetyl) transferase 121851205349,76765.928.65Protein modificationIntegral to membrane
    GFAPGlial fibrillary acidic protein12113549,85062.635.42NACytoplasm
    GMDSGDP-mannose 4,6 dehydratase908714741,92394.216.87+++Leukocyte adhesionCytoplasm
    GNPDA1Glucosamine-6-phosphate deaminase 1117163932,64897.426.32+++Carbohydrate metabolismCytoplasm
    H1FOOHistone H1oo protein7476250335,79298.214.22–4.52MeiosisCytoplasm
    HNRNPMHeterogeneous nuclear ribonucleoprotein M5597774777,46498.588.84mRNA splicingNucleus
    HRGHistidine-rich glycoprotein12352359,5411007.09Blood coagulationExtracellular
    KIAA1370Uncharacterized protein166218826121,59495.198.12NANA
    KLC2Kinesin light chain 21387855368,89266.706.72++TransportCytoplasm
    KRT1Keratin, type II cytoskeletal 123805440665,9991008.15++, +++Oxidative responseMembrane
    KRT2Keratin, type II cytoskeletal 223993865065,39382.928.07+++KeratinizationIntermediate
    KRT6AKeratin, type II 6A134634460,00899.898.09+, +++Cell differentiationKeratin filament
    KRT6BKeratin, type II 6B23805440460,03099.028.09+Cell differentiationIntermediate
    KRT6CKeratin, type II 6C5980308959,98898.798.09+Cell differentiationIntermediate
    KRT9Keratin, type I cytoskeletal 923993888662,027100.005.14− to +++Intermediate filament organizationIntermediate
    KRT10Keratin, type I cytoskeletal 1026984976958,79298.045.13−, +++Cell proliferationIntermediate
    KRT14Keratin, type I cytoskeletal 1422946304451,52999.775.09+Cell proliferationIntermediate
    KRT15Keratin, type I cytoskeletal 1521654846049,16777.484.71Epidermis developmentIntermediate
    KRT16Keratin, type I cytoskeletal 162350307551,23687.634.99−, +Epidermis developmentIntermediate
    KRT25Keratin, type I cytoskeletal 257472331649,28778.505Epidermis developmentIntermediate
    MED14Mediator complex subunit 14145559461160,50487.638.97Transcription regulationNucleus
    MSH2MutS protein homolog 21171032104,67792.015.58DNA repairNucleus
    MYO1CMyosin-1c226694178121,64871.659.48+++TransportMembrane
    MEF2CMyocyte-specific enhancer factor 2C250087551,18972.308.14Transcription regulationNucleus
    MYL2Myosin light chain 214906774917,67089.334.96Immune responseCytoplasm
    MYH11Myosin heavy chain 1113432177227,19993.045.42Cardiac muscleMyosin
    NDEL1Nuclear distribution nudE-17472500638,35261.764.22–4.52TransportCytoplasm
    NRAPNebulin-related anchoring protein115502505196,95079.939.24Ribosomal biogenesisNucleus
    NUMA1Nuclear mitotic apparatus protein 1145559510238,11595.905.63− to +++Nucleus organizationCytoplasm
    OSBPL8Oxysterol-binding protein 839932732101,13295.407.24–7.54+++TransportNA
    PCID2PCI domain-containing protein 28568103446,00099.998.78NANA
    PCNTPericentrin188595720377,85093.655.39CytoskeletalCytoplasm
    PDE4APhosphodiesterase 4A11624270698,08170.995.09Signal transductionMembrane
    PHB2Prohibitin-27475215133,2761003.92–4.22+++TranscriptionCytoplasm
    PLGPlasminogen13031690,51063.487.04Tissue remodelingExtracellular
    RNF115RING finger protein 1155640538933,68265.135.39+++Ubl conjugationCytoplasm
    RTEL1Regulator of telomere elongation helicase 1229462743133,59972.308.6DNA repairNucleus
    SERPINA3Serpin peptidase inhibitor A311287447,62199.887.24–7.54++, +++Acute phase responseNucleus
    SERPINC1Serpin peptidase inhibitor C111393652,5691006.32+++Blood coagulationExtracellular
    SLIRPSRA stem-loop-interacting RNA-binding protein7476272312,34123.7010.25+TranscriptionMitochondria
    SMC1AStructural maintenance of chromosomes protein 1A29336622143,14495.717.51+++DNA repairNucleus
    TMF1TATA modulatory factor 1218511858122,76765.134.88Transcription regulationNucleus
    TRIB1Tribbles homolog 18330592940,98399.166.86Response to LPSCytoplasm
    VCLVinculin21903479123,72297.365.5+++Muscle contractionExtracellular
    VIMVimentin14902111658,00092.159.8Host-pathogen interactionCytoplasm
    ZBTB43Zinc finger and BTB-432339697652,59790.405.46NANA
    ZNF248Zinc finger protein 2484760629967,04478.508.59Transcription regulationNucleus
    ZNF840Zinc finger protein 84021851215983,18183.319.69Transcription regulationNucleus
    FLJ45035Uncharacterized protein7471096815,48895.197.41NANA