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1.

Interpretation of shotgun proteomic data: the protein inference problem.

Nesvizhskii AI, Aebersold R.

Mol Cell Proteomics. 2005 Oct;4(10):1419-40. Epub 2005 Jul 11.

2.

Elective affinities--bioinformatic analysis of proteomic mass spectrometry data.

Li X, Pizarro A, Grosser T.

Arch Physiol Biochem. 2009 Dec;115(5):311-9. doi: 10.3109/13813450903390039. Review.

PMID:
19911947
3.

Detection and validation of non-synonymous coding SNPs from orthogonal analysis of shotgun proteomics data.

Bunger MK, Cargile BJ, Sevinsky JR, Deyanova E, Yates NA, Hendrickson RC, Stephenson JL Jr.

J Proteome Res. 2007 Jun;6(6):2331-40. Epub 2007 May 9.

PMID:
17488105
5.

Protein identification by tandem mass spectrometry and sequence database searching.

Nesvizhskii AI.

Methods Mol Biol. 2007;367:87-119. Review.

PMID:
17185772
6.

A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.

MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd.

Anal Chem. 2003 Dec 15;75(24):6912-21.

PMID:
14670053
7.

VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins.

Matthiesen R, Trelle MB, Højrup P, Bunkenborg J, Jensen ON.

J Proteome Res. 2005 Nov-Dec;4(6):2338-47.

PMID:
16335983
8.

Informatics for protein identification by mass spectrometry.

Johnson RS, Davis MT, Taylor JA, Patterson SD.

Methods. 2005 Mar;35(3):223-36. Epub 2005 Jan 13. Review.

PMID:
15722219
9.

Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra.

Yen CY, Russell S, Mendoza AM, Meyer-Arendt K, Sun S, Cios KJ, Ahn NG, Resing KA.

Anal Chem. 2006 Feb 15;78(4):1071-84.

PMID:
16478097
10.

Analysing proteomic data.

Barrett J, Brophy PM, Hamilton JV.

Int J Parasitol. 2005 Apr 30;35(5):543-53. Review.

PMID:
15826646
11.

Computational approaches to peptide identification via tandem MS.

Hubbard SJ.

Methods Mol Biol. 2010;604:23-42. doi: 10.1007/978-1-60761-444-9_3.

PMID:
20013362
12.

Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics.

Resing KA, Meyer-Arendt K, Mendoza AM, Aveline-Wolf LD, Jonscher KR, Pierce KG, Old WM, Cheung HT, Russell S, Wattawa JL, Goehle GR, Knight RD, Ahn NG.

Anal Chem. 2004 Jul 1;76(13):3556-68.

PMID:
15228325
13.

STEM: a software tool for large-scale proteomic data analyses.

Shinkawa T, Taoka M, Yamauchi Y, Ichimura T, Kaji H, Takahashi N, Isobe T.

J Proteome Res. 2005 Sep-Oct;4(5):1826-31.

PMID:
16212438
14.

Shotgun protein identification and quantification by mass spectrometry in neuroproteomics.

Lu B, Xu T, Park SK, McClatchy DB, Liao L, Yates JR 3rd.

Methods Mol Biol. 2009;566:229-59. doi: 10.1007/978-1-59745-562-6_16.

PMID:
20058176
15.

DBParser: web-based software for shotgun proteomic data analyses.

Yang X, Dondeti V, Dezube R, Maynard DM, Geer LY, Epstein J, Chen X, Markey SP, Kowalak JA.

J Proteome Res. 2004 Sep-Oct;3(5):1002-8.

PMID:
15473689
16.

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides.

Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS.

J Proteome Res. 2005 Nov-Dec;4(6):2273-82.

PMID:
16335976
17.

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

Bandeira N, Clauser KR, Pevzner PA.

Mol Cell Proteomics. 2007 Jul;6(7):1123-34. Epub 2007 Apr 19.

18.

Recent developments in proteome informatics for mass spectrometry analysis.

Wright JC, Hubbard SJ.

Comb Chem High Throughput Screen. 2009 Feb;12(2):194-202. Review.

PMID:
19199887
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