Aebersold R, Mann M: Mass spectrometry-based proteomics. Nature 2003, 422(6928):198–207. 10.1038/nature01511
Article
CAS
PubMed
Google Scholar
Nesvizhskii AI, Vitek O, Aebersold R: Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007, 4(10):787–797. 10.1038/nmeth1088
Article
CAS
PubMed
Google Scholar
Nesvizhskii AI, Vitek O, Aebersold R: Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods 2007, 4(10):787–797. 10.1038/nmeth1088
Article
CAS
PubMed
Google Scholar
Wu L, Hwang SI, Rezaul K, Lu LJ, Mayya V, Gerstein M, Eng JK, Lundgren DH, Han DK: Global survey of human T leukemic cells by integrating proteomics and transcriptomics profiling. Mol Cell Proteomics 2007, 6(8):1343–1353. 10.1074/mcp.M700017-MCP200
Article
CAS
PubMed
Google Scholar
Cox J, Mann M: MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26(12):1367–1372. 10.1038/nbt.1511
Article
CAS
PubMed
Google Scholar
Slebos RJ, Brock JW, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, et al.: Evaluation of Strong Cation Exchange versus Isoelectric Focusing of Peptides for Multidimensional Liquid Chromatography-Tandem Mass Spectrometry. J Proteome Res 2008.
Google Scholar
Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R: Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics 2006, 5(4):652–670.
Article
CAS
PubMed
Google Scholar
Ning K, Fermin D, Nesvizhskii AI: Computational analysis of unassigned high quality MS/MS spectra in proteomic datasets. Proteomics 2010.
Google Scholar
Edwards NJ: Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol Syst Biol 2007, 3: 102.
PubMed Central
PubMed
Google Scholar
Kersey PJ, Duarte J, Williams A, Karavidopoulou Y, Birney E, Apweiler R: The International Protein Index: an integrated database for proteomics experiments. Proteomics 2004, 4(7):1985–1988. 10.1002/pmic.200300721
Article
CAS
PubMed
Google Scholar
Castle JC, Zhang C, Shah JK, Kulkarni AV, Kalsotra A, Cooper TA, Johnson JM: Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 2008, 40(12):1416–1425. 10.1038/ng.264
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB: Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456(7221):470–476. 10.1038/nature07509
Article
PubMed Central
CAS
PubMed
Google Scholar
Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ: Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol 2006, 7(4):R35. 10.1186/gb-2006-7-4-r35
Article
PubMed Central
PubMed
Google Scholar
Chang KY, Georgianna DR, Heber S, Payne GA, Muddiman DC: Detection of Alternative Splice Variants at the Proteome Level in Aspergillus flavus. J Proteome Res
Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R: Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data - Toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Molecular & Cellular Proteomics 2006, 5(4):652–670. 10.1074/mcp.M500319-MCP200
Article
CAS
Google Scholar
Boguski MS, Lowe TM, Tolstoshev CM: dbEST--database for "expressed sequence tags". Nat Genet 1993, 4(4):332–333. 10.1038/ng0893-332
Article
CAS
PubMed
Google Scholar
Aaronson JS, Eckman B, Blevins RA, Borkowski JA, Myerson J, Imran S, Elliston KO: Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res 1996, 6(9):829–845. 10.1101/gr.6.9.829
Article
CAS
PubMed
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621–628. 10.1038/nmeth.1226
Article
CAS
PubMed
Google Scholar
Mo F, Hong X, Gao F, Du L, Wang J, Omenn GS, Lin B: A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC Bioinformatics 2008, 9(1):537. 10.1186/1471-2105-9-537
Article
PubMed Central
PubMed
Google Scholar
Power KA, McRedmond JP, de Stefani A, Gallagher WM, Gaora PO: High-throughput proteomics detection of novel splice isoforms in human platelets. PLoS One 2009, 4(3):e5001. 10.1371/journal.pone.0005001
Article
PubMed Central
PubMed
Google Scholar
Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2008.
Google Scholar
Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009.
Google Scholar
Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R: The PeptideAtlas project. Nucleic Acids Res 2006, 34(Database issue):D655–658. 10.1093/nar/gkj040
Article
PubMed Central
CAS
PubMed
Google Scholar
Birzele F, Csaba G, Zimmer R: Alternative splicing and protein structure evolution. Nucl Acids Res 2008, 36(2):550–558. 10.1093/nar/gkm1054
Article
PubMed Central
CAS
PubMed
Google Scholar
Melamud E, Moult J: Stochastic noise in splicing machinery. Nucl Acids Res 2009, 37(14):4873–4886. 10.1093/nar/gkp471
Article
PubMed Central
CAS
PubMed
Google Scholar
Craig R, Beavis RC: TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9):1466–1467. 10.1093/bioinformatics/bth092
Article
CAS
PubMed
Google Scholar
MacLean B, Eng JK, Beavis RC, McIntosh M: General framework for developing and evaluating database scoring algorithms using the TANDEM search engine. Bioinformatics 2006, 22(22):2830–2832. 10.1093/bioinformatics/btl379
Article
CAS
PubMed
Google Scholar
Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C, Boneh A, Chen WK, et al.: A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008, 134(1):112–123. 10.1016/j.cell.2008.06.016
Article
PubMed Central
CAS
PubMed
Google Scholar
Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2007, 35(Database issue):D26–31. 10.1093/nar/gkl993
Article
PubMed Central
CAS
PubMed
Google Scholar
Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, et al.: The UCSC Genome Browser Database. Nucleic Acids Res 2003, 31(1):51–54. 10.1093/nar/gkg129
Article
PubMed Central
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389–3402. 10.1093/nar/25.17.3389
Article
PubMed Central
CAS
PubMed
Google Scholar
Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG: Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics. Mol Cell Proteomics 2005, 4(10):1487–1502. 10.1074/mcp.M500084-MCP200
Article
CAS
PubMed
Google Scholar
Zybailov B, Coleman MK, Florens L, Washburn MP: Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Analytical Chemistry 2005, 77(19):6218–6224. 10.1021/ac050846r
Article
CAS
PubMed
Google Scholar