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References for PMC Articles for PubMed (Select 21813416)


A support vector machine model for the prediction of proteotypic peptides for accurate mass and time proteomics.

Webb-Robertson BJ, Cannon WR, Oehmen CS, Shah AR, Gurumoorthi V, Lipton MS, Waters KM.

Bioinformatics. 2010 Jul 1;26(13):1677-83.


BLAST+: architecture and applications.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL.

BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421.


High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.

Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R.

Nat Methods. 2010 Jan;7(1):43-6. doi: 10.1038/nmeth.1408. Epub 2009 Dec 6.


Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans.

Malmström J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R.

Nature. 2009 Aug 6;460(7256):762-5. doi: 10.1038/nature08184. Epub 2009 Jul 15.


The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions.

Tao L, Dahl DB, Pérez LM, Russell DH.

J Am Soc Mass Spectrom. 2009 Sep;20(9):1593-602. doi: 10.1016/j.jasms.2009.04.018. Epub 2009 May 5.


Prediction of high-responding peptides for targeted protein assays by mass spectrometry.

Fusaro VA, Mani DR, Mesirov JP, Carr SA.

Nat Biotechnol. 2009 Feb;27(2):190-8. doi: 10.1038/nbt.1524. Epub 2009 Jan 25.


Support vector machines and kernels for computational biology.

Ben-Hur A, Ong CS, Sonnenburg S, Schölkopf B, Rätsch G.

PLoS Comput Biol. 2008 Oct;4(10):e1000173. doi: 10.1371/journal.pcbi.1000173. Epub 2008 Oct 31. Review. No abstract available.


PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows.

Deutsch EW, Lam H, Aebersold R.

EMBO Rep. 2008 May;9(5):429-34. doi: 10.1038/embor.2008.56. Review.


Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform.

Pan S, Rush J, Peskind ER, Galasko D, Chung K, Quinn J, Jankovic J, Leverenz JB, Zabetian C, Pan C, Wang Y, Oh JH, Gao J, Zhang J, Montine T, Zhang J.

J Proteome Res. 2008 Feb;7(2):720-30. doi: 10.1021/pr700630x. Epub 2008 Jan 11.


Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics.

Mirzaei H, McBee JK, Watts J, Aebersold R.

Mol Cell Proteomics. 2008 Apr;7(4):813-23. Epub 2007 Dec 17.


Prediction of peptides observable by mass spectrometry applied at the experimental set level.

Sanders WS, Bridges SM, McCarthy FM, Nanduri B, Burgess SC.

BMC Bioinformatics. 2007 Nov 1;8 Suppl 7:S23.


AAindex: amino acid index database, progress report 2008.

Kawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M.

Nucleic Acids Res. 2008 Jan;36(Database issue):D202-5. Epub 2007 Nov 12.


Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT.

Rivers J, Simpson DM, Robertson DH, Gaskell SJ, Beynon RJ.

Mol Cell Proteomics. 2007 Aug;6(8):1416-27. Epub 2007 May 17.


Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes.

Pratt JM, Simpson DM, Doherty MK, Rivers J, Gaskell SJ, Beynon RJ.

Nat Protoc. 2006;1(2):1029-43.


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.


Computational prediction of proteotypic peptides for quantitative proteomics.

Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R.

Nat Biotechnol. 2007 Jan;25(1):125-31. Epub 2006 Dec 31.


A computational approach toward label-free protein quantification using predicted peptide detectability.

Tang H, Arnold RJ, Alves P, Xun Z, Clemmer DE, Novotny MV, Reilly JP, Radivojac P.

Bioinformatics. 2006 Jul 15;22(14):e481-8.


Effects of sequestration on signal transduction cascades.

Blüthgen N, Bruggeman FJ, Legewie S, Herzel H, Westerhoff HV, Kholodenko BN.

FEBS J. 2006 Mar;273(5):895-906.


Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides.

Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ.

Nat Methods. 2005 Aug;2(8):587-9.


Discovery of biomarker candidates within disease by protein profiling: principles and concepts.

Marko-Varga G, Lindberg H, Löfdahl CG, Jönsson P, Hansson L, Dahlbäck M, Lindquist E, Johansson L, Foster M, Fehniger TE.

J Proteome Res. 2005 Jul-Aug;4(4):1200-12.

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