PubMed

In silico proteome analysis to facilitate proteomics experiments using mass spectrometry.

Cagney G, Amiri S, Premawaradena T, Lindo M, Emili A.

Proteome Sci. 2003 Aug 13;1(1):5.PMID: 12946274 [PubMed - as supplied by publisher]Related articlesFree article

IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry.

Lu D, Liu RZ, Izumi V, Fenstermacher D, Haura EB, Koomen J, Eschrich SA.

Bioinformatics. 2008 Dec 1;24(23):2801-2. Epub 2008 Oct 7.PMID: 18842605 [PubMed - indexed for MEDLINE]Related articlesFree article

The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.

Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R.

BMC Bioinformatics. 2008 Dec 9;9:529.PMID: 19068132 [PubMed - indexed for MEDLINE]Related articlesFree article

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542.PMID: 19087345 [PubMed - indexed for MEDLINE]Related articlesFree article

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 [PubMed - indexed for MEDLINE]Related articles

Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring.

Dworzanski JP, Snyder AP, Chen R, Zhang H, Wishart D, Li L.

Anal Chem. 2004 Apr 15;76(8):2355-66.PMID: 15080748 [PubMed - indexed for MEDLINE]Related articles

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells.

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard JP, Monsarrat B.

Mol Cell Proteomics. 2007 Sep;6(9):1621-37. Epub 2007 May 28.PMID: 17533220 [PubMed - indexed for MEDLINE]Related articlesFree article

Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.

Wang G, Wu WW, Zeng W, Chou CL, Shen RF.

J Proteome Res. 2006 May;5(5):1214-23.PMID: 16674111 [PubMed - indexed for MEDLINE]Related articles

Analysis of the Arabidopsis cytosolic ribosome proteome provides detailed insights into its components and their post-translational modification.

Carroll AJ, Heazlewood JL, Ito J, Millar AH.

Mol Cell Proteomics. 2008 Feb;7(2):347-69. Epub 2007 Oct 13.PMID: 17934214 [PubMed - indexed for MEDLINE]Related articlesFree article

High-throughput analysis of rat liver plasma membrane proteome by a nonelectrophoretic in-gel tryptic digestion coupled with mass spectrometry identification.

Cao R, He Q, Zhou J, He Q, Liu Z, Wang X, Chen P, Xie J, Liang S.

J Proteome Res. 2008 Feb;7(2):535-45. Epub 2008 Jan 1.PMID: 18166008 [PubMed - indexed for MEDLINE]Related articles

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 [PubMed - indexed for MEDLINE]Related articles

Absolute quantification strategies in proteomics based on mass spectrometry.

Brönstrup M.

Expert Rev Proteomics. 2004 Dec;1(4):503-12. Review.PMID: 15966845 [PubMed - indexed for MEDLINE]Related articles

MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences.

Barsnes H, Mikalsen SO, Eidhammer I.

BMC Bioinformatics. 2006 Jan 26;7:42.PMID: 16438723 [PubMed - indexed for MEDLINE]Related articlesFree article

Quantify this! Report on a round table discussion on quantitative mass spectrometry in proteomics.

Quadroni M, Ducret A, Stöcklin R.

Proteomics. 2004 Aug;4(8):2211-5.PMID: 15274113 [PubMed - indexed for MEDLINE]Related articles

A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome.

Duan X, Young R, Straubinger RM, Page B, Cao J, Wang H, Yu H, Canty JM, Qu J.

J Proteome Res. 2009 Jun;8(6):2838-50.PMID: 19290621 [PubMed - indexed for MEDLINE]Related articlesFree article

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments.

Allmer J, Kuhlgert S, Hippler M.

BMC Bioinformatics. 2008 Jul 7;9:302.PMID: 18605993 [PubMed - indexed for MEDLINE]Related articlesFree article

Current chemical tagging strategies for proteome analysis by mass spectrometry.

Leitner A, Lindner W.

J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Dec 25;813(1-2):1-26. Review.PMID: 15556511 [PubMed - indexed for MEDLINE]Related articles

Comparison of indirect and direct approaches using ion-trap and Fourier transform ion cyclotron resonance mass spectrometry for exploring viperid venom proteomes.

Fox JW, Ma L, Nelson K, Sherman NE, Serrano SM.

Toxicon. 2006 May;47(6):700-14. Epub 2006 Mar 30.PMID: 16574175 [PubMed - indexed for MEDLINE]Related articles

Analysing proteomic data.

Barrett J, Brophy PM, Hamilton JV.

Int J Parasitol. 2005 Apr 30;35(5):543-53. Review.PMID: 15826646 [PubMed - indexed for MEDLINE]Related articles

Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

Siepen JA, Keevil EJ, Knight D, Hubbard SJ.

J Proteome Res. 2007 Jan;6(1):399-408.PMID: 17203985 [PubMed - indexed for MEDLINE]Related articlesFree article