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Items: 1 to 20 of 114

1.

Automatic validation of phosphopeptide identifications from tandem mass spectra.

Lu B, Ruse C, Xu T, Park SK, Yates J 3rd.

Anal Chem. 2007 Feb 15;79(4):1301-10.

2.

Automatic validation of phosphopeptide identifications by the MS2/MS3 target-decoy search strategy.

Jiang X, Han G, Feng S, Jiang X, Ye M, Yao X, Zou H.

J Proteome Res. 2008 Apr;7(4):1640-9. doi: 10.1021/pr700675j. Epub 2008 Mar 4.

PMID:
18314942
3.

Colander: a probability-based support vector machine algorithm for automatic screening for CID spectra of phosphopeptides prior to database search.

Lu B, Ruse CI, Yates JR 3rd.

J Proteome Res. 2008 Aug;7(8):3628-34. doi: 10.1021/pr8001194. Epub 2008 Jun 19.

4.

Prophossi: automating expert validation of phosphopeptide-spectrum matches from tandem mass spectrometry.

Martin DM, Nett IR, Vandermoere F, Barber JD, Morrice NA, Ferguson MA.

Bioinformatics. 2010 Sep 1;26(17):2153-9. doi: 10.1093/bioinformatics/btq341. Epub 2010 Jul 22.

5.

Correction of errors in tandem mass spectrum extraction enhances phosphopeptide identification.

Hao P, Ren Y, Tam JP, Sze SK.

J Proteome Res. 2013 Dec 6;12(12):5548-57. doi: 10.1021/pr4004486. Epub 2013 Nov 4.

PMID:
24147958
6.

Reference-facilitated phosphoproteomics: fast and reliable phosphopeptide validation by microLC-ESI-Q-TOF MS/MS.

Imanishi SY, Kochin V, Ferraris SE, de Thonel A, Pallari HM, Corthals GL, Eriksson JE.

Mol Cell Proteomics. 2007 Aug;6(8):1380-91. Epub 2007 May 17.

7.

A hierarchical MS2/MS3 database search algorithm for automated analysis of phosphopeptide tandem mass spectra.

Xu H, Wang L, Sallans L, Freitas MA.

Proteomics. 2009 Apr;9(7):1763-70. doi: 10.1002/pmic.200800282.

8.

Importance of manual validation for the identification of phosphopeptides using a linear ion trap mass spectrometer.

Goldstrohm DA, Broeckling CD, Prenni JE, Curthoys NP.

J Biomol Tech. 2011 Apr;22(1):10-20.

9.

Quality assessment of tandem mass spectra using support vector machine (SVM).

Zou AM, Wu FX, Ding JR, Poirier GG.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S49. doi: 10.1186/1471-2105-10-S1-S49.

10.

Support vector machines for improved peptide identification from tandem mass spectrometry database search.

Webb-Robertson BJ.

Methods Mol Biol. 2009;492:453-60. doi: 10.1007/978-1-59745-493-3_28.

PMID:
19241051
11.

Integrated data management and validation platform for phosphorylated tandem mass spectrometry data.

Lahesmaa-Korpinen AM, Carlson SM, White FM, Hautaniemi S.

Proteomics. 2010 Oct;10(19):3515-24. doi: 10.1002/pmic.200900727.

12.
13.

Automated phosphopeptide identification using multiple MS/MS fragmentation modes.

Vandenbogaert M, Hourdel V, Jardin-Mathé O, Bigeard J, Bonhomme L, Legros V, Hirt H, Schwikowski B, Pflieger D.

J Proteome Res. 2012 Dec 7;11(12):5695-703. doi: 10.1021/pr300507j. Epub 2012 Nov 7.

PMID:
23094866
14.

Universal and confident phosphorylation site localization using phosphoRS.

Taus T, Köcher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K.

J Proteome Res. 2011 Dec 2;10(12):5354-62. doi: 10.1021/pr200611n. Epub 2011 Nov 10.

PMID:
22073976
16.

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI.

Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5.

17.

Comparison of alternative MS/MS and bioinformatics approaches for confident phosphorylation site localization.

Wiese H, Kuhlmann K, Wiese S, Stoepel NS, Pawlas M, Meyer HE, Stephan C, Eisenacher M, Drepper F, Warscheid B.

J Proteome Res. 2014 Feb 7;13(2):1128-37. doi: 10.1021/pr400402s. Epub 2014 Jan 3.

PMID:
24364495
18.
19.

Effect of high-accuracy precursor masses on phosphopeptide identification from MS3 spectra.

Timm W, Ozlu N, Steen JJ, Steen H.

Anal Chem. 2010 May 15;82(10):3977-80. doi: 10.1021/ac100118u.

PMID:
20426395
20.

An SVM scorer for more sensitive and reliable peptide identification via tandem mass spectrometry.

Wang H, Fu Y, Sun R, He S, Zeng R, Gao W.

Pac Symp Biocomput. 2006:303-14.

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