Profiling proteoforms: promising follow-up of proteomics for biomarker discovery

References

• Zhang Z, Bast RC, Yu Y, et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res 2004;64(16):5882-90
   PubMed Web of Science ®Google Scholar
• Li XJ, Hayward C, Fong PY, et al. A blood-based proteomic classifier for the molecular characterization of pulmonary nodules. Sci Transl Med 2013;5(207):207ra142
   PubMed Web of Science ®Google Scholar
• Smith LM, Kelleher NL. Proteoform: a single term describing protein complexity. Nat Methods 2013;10(3):186-7
   PubMed Web of Science ®Google Scholar
• Tang W, Fei Y, Page M. Biological significance of RNA editing in cells. Mol Biotechnol 2012;52(1):91-100
   PubMedGoogle Scholar
• Stratton M, Campbell P, Futreal P. The cancer genome. Nature 2009;458(7239):719-24
   PubMed Web of Science ®Google Scholar
• Li J, Su Z, Ma Z-Q, et al. A bioinformatics workflow for variant peptide detection in shotgun proteomics. Mol Cell Proteomics 2011;10(5):M110.006536
   PubMed Web of Science ®Google Scholar
• Tran JC, Zamdborg L, Ahlf DR, et al. Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 2011;480(7376):254-8
   PubMed Web of Science ®Google Scholar
• Nedelkov D, Kiernan UA, Niederkofler EE, et al. Population proteomics: the concept, attributes, and potential for cancer biomarker research. Mol Cell Proteomics 2006;5(10):1811-18
   PubMed Web of Science ®Google Scholar
• Nedelkov D, Kiernan UA, Niederkofler EE, et al. Investigating diversity in human plasma proteins. Proc Natl Acad Sci USA 2005;102(31):10852-7
   PubMed Web of Science ®Google Scholar
• Li M, Durbin KR, Sweet SMM, et al. Oncogene-induced cellular senescence elicits an anti-Warburg effect. Proteomics 2013;13(17):2585-96
   PubMedGoogle Scholar
• Archakov A, Zgoda V, Kopylov A, et al. Chromosome-centric approach to overcoming bottlenecks in the Human Proteome Project. Exp Rev Proteomics 2012;9(6):667-76
   PubMed Web of Science ®Google Scholar
• Veenstra TD. Where are all the biomarkers? Exp Rev Proteomics 2011;8(6):681-3
   PubMed Web of Science ®Google Scholar
• Ning K, Nesvizhskii AI. The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. BMC Bioinformatics 2010;11(Suppl 1):S14
   PubMedGoogle Scholar
• Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol Cell Proteomics 2010;9(1):184-96
   PubMed Web of Science ®Google Scholar
• Kopylov AT, Zgoda VG, Lisitsa AV, Archakov AI. Combined use of irreversible binding and MRM technology for low- and ultralow copy-number protein detection and quantitation. Proteomics 2013;13(5):727-42
   PubMedGoogle Scholar
• Wiśniewski JR, Ostasiewicz P, Duś K, et al. Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma. Mol Syst Biol 2012;8:611
   PubMed Web of Science ®Google Scholar
• Ingram VM. Gene mutations in human haemoglobin: the chemical difference between normal and sickle cell haemoglobin. Nature 1957;180(4581):326-8
   PubMed Web of Science ®Google Scholar
• Coelho Graça D, Lescuyer P, Clerici L, et al. Electron transfer dissociation mass spectrometry of hemoglobin on clinical samples. J Am Soc Mass Spectrom 2012;23(10):1750-6
   PubMedGoogle Scholar
• Bunger MK, Cargile BJ, Sevinsky JR, et al. Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data. J Proteome Res 2007;6(6):2331-40
   PubMedGoogle Scholar
• Wheeler DA, Wang L. From human genome to cancer genome: the first decade. Genome Res 2013;23(7):1054-62
   PubMed Web of Science ®Google Scholar
• Li J, Duncan DT, Zhang B. CanProVar: a human cancer proteome variation database. Hum Mutat 2010;31(3):219-28
   PubMed Web of Science ®Google Scholar
• Shepherd R, Forbes SA, Beare D, et al. Data mining using the Catalogue of Somatic Mutations in Cancer BioMart. Database 2011;2011:bar018
   PubMedGoogle Scholar
• Jennings J, Hudson TJ. Reflections on the founding of the International Cancer Genome Consortium. Clin Chem 2013;59(1):18-21
   PubMedGoogle Scholar
• Wu J-R, Zeng R. Molecular basis for population variation: from SNPs to SAPs. FEBS Lett 2012;586(18):2841-5
   PubMed Web of Science ®Google Scholar
• Takeshita H, Fujihara J, Ueki M, et al. Nonsynonymous single-nucleotide polymorphisms of the human apoptosis-related endonuclease-DNA fragmentation factor beta polypeptide, endonuclease G, and Flap endonuclease-1-genes show a low degree of genetic heterogeneity. DNA Cell Biol 2012;31(1):36-42
   PubMedGoogle Scholar
• Su Z-D, Sun L, Yu D-X, et al. Quantitative detection of single amino acid polymorphisms by targeted proteomics. J Mol Cell Biol 2011;3(5):309-15
   PubMed Web of Science ®Google Scholar
• Wang Q, Chaerkady R, Wu J, et al. Mutant proteins as cancer-specific biomarkers. Proc Natl Acad Sci USA 2011;108(6):2444-9
   PubMed Web of Science ®Google Scholar
• The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487(7407):330-7
   PubMed Web of Science ®Google Scholar
• Xin F, Radivojac P. Post-translational modifications induce significant yet not extreme changes to protein structure. Bioinformatics 2012;28(22):2905-13
   PubMedGoogle Scholar
• Vizcaíno JA, Côté RG, Csordas A, et al. The proteomics identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2013;41(Database issue):D1063-9
   PubMed Web of Science ®Google Scholar
• Gholami AM, Hahne H, Wu Z, et al. Global proteome analysis of the NCI-60 cell line panel. Cell Reports 2013;4(3):609-20
   PubMed Web of Science ®Google Scholar
• Bollag G, Hirth P, Tsai J, et al. Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature 2010;467(7315):596-9
   PubMed Web of Science ®Google Scholar
• Miura K, Fujibuchi W, Unno M. Splice isoforms as therapeutic targets for colorectal cancer. Carcinogenesis 2012;33(12):2311-19
   PubMed Web of Science ®Google Scholar
• Omenn GS, Menon R, Zhang Y. Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteomics 2013;90:28-37
   PubMed Web of Science ®Google Scholar
• Menon R, Omenn GS. Proteomic characterization of novel alternative splice variant proteins in human epidermal growth factor receptor 2/neu-induced breast cancers. Cancer Res 2010;70(9):3440-9
   PubMed Web of Science ®Google Scholar
• Menon R, Zhang Q, Zhang Y, et al. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res 2009;69(1):300-9
   PubMed Web of Science ®Google Scholar
• Omenn GS, Yocum AK, Menon R. Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications. Dis Markers 2010;28(4):241-51
   PubMedGoogle Scholar
• Liu X, Jin Z, O'Brien R, et al. Constrained selected reaction monitoring: quantification of selected post-translational modifications and protein isoforms. Methods 2013;61(3):304-12
   PubMed Web of Science ®Google Scholar
• Wu J, Pungaliya P, Kraynov E, Bates B. Identification and quantification of osteopontin splice variants in the plasma of lung cancer patients using immunoaffinity capture and targeted mass spectrometry. Biomarkers 2012;17(2):125-33
   PubMed Web of Science ®Google Scholar
• Madian AG, Rochelle NS, Regnier FE. Mass-linked immuno-selective assays in targeted proteomics. Anal Chem 2013;85(2):737-48
   PubMedGoogle Scholar
• Archakov A, Ivanov Y, Lisitsa A, Zgoda V. Biospecific irreversible fishing coupled with atomic force microscopy for detection of extremely low-abundant proteins. Proteomics 2009;9(5):1326-43
   PubMedGoogle Scholar
• Liddy KA, White MY, Cordwell SJ. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics. Genome Med 2013;5(2):20
   PubMedGoogle Scholar
• Yates JR, Kelleher NL. Top down proteomics. Anal Chem 2013;85(13):6151
   PubMedGoogle Scholar
• Nedelkov D. Population proteomics: investigation of protein diversity in human populations. Proteomics 2008;8(4):779-86
   PubMed Web of Science ®Google Scholar
• Vaudel M, Sickmann A, Martens L. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics. Biochim Biophys Acta 2013;1844(1 Pt A):12-20
   PubMedGoogle Scholar
• Ossola R, Schiess R, Picotti P, et al. Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites. Methods Mol Biol 2011;728:179-94
   PubMedGoogle Scholar
• Balasubramaniam D, Eissler CL, Stauffacher CV, Hall MC. Use of selected reaction monitoring data for label-free quantification of protein modification stoichiometry. Proteomics 2010;10(23):4301-5
   PubMedGoogle Scholar
• Mayor U, Peng J. Deciphering tissue-specific ubiquitylation by mass spectrometry. Methods Mol Biol 2012;832:65-80
   PubMedGoogle Scholar
• Kettenbach AN, Rush J, Gerber SA. Absolute quantification of protein and post-translational modification abundance with stable isotope-labeled synthetic peptides. Nat Protoc 2011;6(2):175-86
   PubMed Web of Science ®Google Scholar
• Zhang P, Kirk JA, Ji W, et al. Multiple reaction monitoring to identify site-specific troponin I phosphorylated residues in the failing human heart. Circulation 2012;126(15):1828-37
   PubMed Web of Science ®Google Scholar
• Agard NJ, Mahrus S, Trinidad JC, et al. Global kinetic analysis of proteolysis via quantitative targeted proteomics. Proc Natl Acad Sci USA 2012;109(6):1913-18
   PubMed Web of Science ®Google Scholar
• Espina V, Mueller C, Edmiston K, et al. Tissue is alive: new technologies are needed to address the problems of protein biomarker pre-analytical variability. Proteomics Clin Appl 2009;3(8):874-82
   PubMedGoogle Scholar
• Rountree CB, Van Kirk CA, You H, et al. Clinical application for the preservation of phospho-proteins through in-situ tissue stabilization. Proteome Sci 2010;8:61
   PubMedGoogle Scholar
• Ponomarenko EA, Lisitsa AV, Petrak J, et al. Identification of differentially expressed proteins using automatic meta-analysis of proteomics-related articles. Biomed Khim 2009;55(1):5-14
   PubMedGoogle Scholar
• Gillery P, Jaisson S. Usefulness of non-enzymatic post-translational modification derived products (PTMDPs) as biomarkers of chronic diseases. J Proteomics 2013;92:228-38
   PubMedGoogle Scholar
• Aebersold R, Burlingame AL, Bradshaw RA. Western blots vs. SRM assays: time to turn the tables? Mol Cell Proteomics 2013;12(9):2381-2
   PubMed Web of Science ®Google Scholar
• Sherman J, Molloy MP, Burlingame AL. Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity. Proteomics 2012;12(8):1147-50
   PubMedGoogle Scholar
• Domon B. Considerations on selected reaction monitoring experiments: implications for the selectivity and accuracy of measurements. Proteomics Clin Appl 2012;6(11-12):609-14
   PubMed Web of Science ®Google Scholar
• Biognosys AG. Available from: www.biognosys.ch
   Google Scholar