Abstract
The human serum proteome is closely associated with the state of the body. Endogenous peptides derived from proteolytic enzymes cleaving on serum proteins are widely studied due to their potential application in disease-specific marker discovery. However, the reproducibility of peptidome analysis of endogenous peptides is significantly influenced by the proteolytic enzymes within body fluids, thereby limiting the clinical use of the endogenous peptides. We comprehensively investigated the N and C terminus of endogenous peptides using peptidomics. The cleavage site patterns of the N and C terminus and adjacent sites from all the identified endogenous peptides were highly conserved under different sample preparation conditions, including long-term incubation at 37°C and pretreatment with repeated freeze-thaw cycles. Furthermore, a distinguishable cleavage site pattern was obtained when a different disease serum was analyzed. The conserved cleavage site pattern derived from proteolytic enzymes holds potential in highly specific disease diagnosis.
Electronic Supplementary Material
The online version of this article (doi:10.1007/s13238-012-2934-4 contains supplementary material, which is available to authorized users.
Keywords: human serum, endogenous peptide, N and C termini, disease diagnosis
Electronic Supplementary Material
Footnotes
Electronic Supplementary Material
The online version of this article (doi:10.1007/s13238-012-2934-4 contains supplementary material, which is available to authorized users.
References
- Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotech. 2008;26:1367–1372. doi: 10.1038/nbt.1511. [DOI] [PubMed] [Google Scholar]
- Diamandis E.P. Peptidomics for cancer diagnosis: present and future. J Proteome Res. 2006;5:2079–2082. doi: 10.1021/pr060225u. [DOI] [PubMed] [Google Scholar]
- Doucet A., Butler G.S., Rodriguez D., Prudova A., Overall C.M. Metadegradomics toward in vivo quantitative degradomics of proteolytic post-translational modifications of the cancer proteome. Mol Cell Proteomics. 2008;7:1925–1951. doi: 10.1074/mcp.R800012-MCP200. [DOI] [PubMed] [Google Scholar]
- Koomen J.M., Li D.H., Xiao L.C., Liu T.C., Coombes K.R., Abbruzzese J., Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling experiments for plasma biomarker discovery. J Proteome Res. 2005;4:972–981. doi: 10.1021/pr050046x. [DOI] [PubMed] [Google Scholar]
- Kresge C.T., Leonowicz M.E., Roth W.J., Vartuli J.C., Beck J.S. Ordered mesoporous molecular sieves synthesized by a liquid-crystal template mechanism. Nature. 1992;359:710–712. doi: 10.1038/359710a0. [DOI] [Google Scholar]
- Nilsson T., Mann M., Aebersold R., Yates J.R., Bairoch A., Bergeron J.J.M. Mass spectrometry in high-throughput proteomics: ready for the big time. Nat Meth. 2010;7:681–685. doi: 10.1038/nmeth0910-681. [DOI] [PubMed] [Google Scholar]
- Rai A.J., Gelfand C.A., Haywood B.C., Warunek D. J., Yi J., Schuchard M.D., Mehigh R.J., Cockrill S.L., Scott G.B.I., Tammen H., et al. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics. 2005;5:3262–3277. doi: 10.1002/pmic.200401245. [DOI] [PubMed] [Google Scholar]
- Ransohoff D.F. Bias as a threat to the validity of cancer molecular-marker research. Nat Rev Cancer. 2005;5:142–149. doi: 10.1038/nrc1550. [DOI] [PubMed] [Google Scholar]
- Schrader M., Schulz-Knappe P. Peptidomics technologies for human body fluids. Trends Biotechnol. 2001;19:55–60. doi: 10.1016/S0167-7799(01)00010-5. [DOI] [PubMed] [Google Scholar]
- Soloviev M., Finch P. Peptidomics: bridging the gap between proteome and metabolome. Proteomics. 2006;6:744–747. doi: 10.1002/pmic.200500878. [DOI] [PubMed] [Google Scholar]
- Tian R.J., Zhang H., Ye M.L., Jiang X.G., Hu L.H., Li X., Bao X.H., Zou H.F. Selective extraction of peptides from human plasma by highly ordered mesoporous silica particles for peptidome analysis. Angew Chem Int Ed. 2007;46:962–965. doi: 10.1002/anie.200603917. [DOI] [PubMed] [Google Scholar]
- Villanueva J., Philip J., Chaparro C.A., Li Y.B., Toledo-Crow R., DeNoyer L., Fleisher M., Robbins R.J., Tempst P. Correcting common errors in identifying cancer-specific serum peptide signatures. J Proteome Res. 2005;4:1060–1072. doi: 10.1021/pr050034b. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Villanueva J., Shaffer D.R., Philip J., Chaparro C.A., Erdjument-Bromage H., Olshen A.B., Fleisher M., Lilja H., Brogi E., Boyd J., Sanchez-Carbayo M., Holland E.C., Cordon-Cardo C., Scher H.I., Tempst P. Differential exoprotease activities confer tumor-specific serum peptidome patterns. J Clin Invest. 2006;116:271–284. doi: 10.1172/JCI26022. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wang F.J., Chen R., Zhu J., Sun D.G., Song C.X., Wu Y.F., Ye M.L., Wang L.M., Zou H.F. A fully automated system with online sample loading, isotope dimethyl labeling and multidimensional separation for high-throughput quantitative proteome analysis. Anal Chem. 2010;82:3007–3015. doi: 10.1021/ac100075y. [DOI] [PubMed] [Google Scholar]
- West-Nielsen M., Høgdall E.V., Marchiori E., Høgdall C.K., Schou C., Heegaard N.H.H. Sample handling for mass spectrometric proteomic investigations of human sera. Anal Chem. 2005;77:5114–5123. doi: 10.1021/ac050253g. [DOI] [PubMed] [Google Scholar]
- Zhu J., Wang F.J., Dong X.L., Ye M.L., Zou H.F. A strategy with label-free quantification of the targeted peptides for quantitative peptidome analysis of human serum. Sci Chin A-Chem. 2010;53:759–767. doi: 10.1007/s11426-010-0127-7. [DOI] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.