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Results: 1 to 20 of 122

1.

A proteomics search algorithm specifically designed for high-resolution tandem mass spectra.

Wenger CD, Coon JJ.

J Proteome Res. 2013 Mar 1;12(3):1377-86. doi: 10.1021/pr301024c. Epub 2013 Jan 31.

PMID:
23323968
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Enhanced peptide identification by electron transfer dissociation using an improved Mascot Percolator.

Wright JC, Collins MO, Yu L, Käll L, Brosch M, Choudhary JS.

Mol Cell Proteomics. 2012 Aug;11(8):478-91. doi: 10.1074/mcp.O111.014522. Epub 2012 Apr 6.

PMID:
22493177
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

MassWiz: a novel scoring algorithm with target-decoy based analysis pipeline for tandem mass spectrometry.

Yadav AK, Kumar D, Dash D.

J Proteome Res. 2011 May 6;10(5):2154-60. doi: 10.1021/pr200031z. Epub 2011 Apr 5.

PMID:
21417338
[PubMed - indexed for MEDLINE]
4.

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions.

Perez-Riverol Y, Sánchez A, Noda J, Borges D, Carvalho PC, Wang R, Vizcaíno JA, Betancourt L, Ramos Y, Duarte G, Nogueira FC, González LJ, Padrón G, Tabb DL, Hermjakob H, Domont GB, Besada V.

Anal Chem. 2013 Apr 2;85(7):3515-20. doi: 10.1021/ac303239g. Epub 2013 Mar 20.

PMID:
23448308
[PubMed - indexed for MEDLINE]
5.

The effects of mass accuracy, data acquisition speed, and search algorithm choice on peptide identification rates in phosphoproteomics.

Bakalarski CE, Haas W, Dephoure NE, Gygi SP.

Anal Bioanal Chem. 2007 Nov;389(5):1409-19. Epub 2007 Sep 14.

PMID:
17874083
[PubMed - indexed for MEDLINE]
6.

Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration.

McHugh LC, Arthur JW.

BMC Bioinformatics. 2010 Sep 6;11:448. doi: 10.1186/1471-2105-11-448.

PMID:
20815925
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

SQID: an intensity-incorporated protein identification algorithm for tandem mass spectrometry.

Li W, Ji L, Goya J, Tan G, Wysocki VH.

J Proteome Res. 2011 Apr 1;10(4):1593-602. doi: 10.1021/pr100959y. Epub 2011 Feb 23.

PMID:
21204564
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA.

Wenger CD, Phanstiel DH, Lee MV, Bailey DJ, Coon JJ.

Proteomics. 2011 Mar;11(6):1064-74. doi: 10.1002/pmic.201000616. Epub 2011 Feb 7.

PMID:
21298793
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

Xiao CL, Chen XZ, Du YL, Sun X, Zhang G, He QY.

J Proteome Res. 2013 Jan 4;12(1):328-35. doi: 10.1021/pr300781t. Epub 2012 Nov 29.

PMID:
23163785
[PubMed - indexed for MEDLINE]
10.

A new probabilistic database search algorithm for ETD spectra.

Sadygov RG, Good DM, Swaney DL, Coon JJ.

J Proteome Res. 2009 Jun;8(6):3198-205. doi: 10.1021/pr900153b.

PMID:
19354237
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A novel algorithm for validating peptide identification from a shotgun proteomics search engine.

Jian L, Niu X, Xia Z, Samir P, Sumanasekera C, Mu Z, Jennings JL, Hoek KL, Allos T, Howard LM, Edwards KM, Weil PA, Link AJ.

J Proteome Res. 2013 Mar 1;12(3):1108-19. doi: 10.1021/pr300631t. Epub 2013 Feb 12.

PMID:
23402659
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

Victor KG, Murgai M, Lyons CE, Templeton TA, Moshnikov SA, Templeton DJ.

J Am Soc Mass Spectrom. 2010 Jan;21(1):80-7. doi: 10.1016/j.jasms.2009.09.007. Epub 2009 Sep 17.

PMID:
19850495
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra.

Ledvina AR, Savitski MM, Zubarev AR, Good DM, Coon JJ, Zubarev RA.

Anal Chem. 2011 Oct 15;83(20):7651-6. doi: 10.1021/ac201843e. Epub 2011 Sep 28.

PMID:
21913643
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A dynamic noise level algorithm for spectral screening of peptide MS/MS spectra.

Xu H, Freitas MA.

BMC Bioinformatics. 2010 Aug 23;11:436. doi: 10.1186/1471-2105-11-436.

PMID:
20731867
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.

Zhang W, Zhang J, Xu C, Li N, Liu H, Ma J, Zhu Y, Xie H.

Proteomics. 2012 Dec;12(23-24):3475-84. doi: 10.1002/pmic.201200017.

PMID:
23081734
[PubMed - indexed for MEDLINE]
16.

Enhanced peptide quantification using spectral count clustering and cluster abundance.

Lee S, Kwon MS, Lee HJ, Paik YK, Tang H, Lee JK, Park T.

BMC Bioinformatics. 2011 Oct 28;12:423. doi: 10.1186/1471-2105-12-423.

PMID:
22034872
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Perez-Riverol Y, Wang R, Hermjakob H, Müller M, Vesada V, Vizcaíno JA.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):63-76. doi: 10.1016/j.bbapap.2013.02.032. Epub 2013 Mar 1. Review.

PMID:
23467006
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

PI: an open-source software package for validation of the SEQUEST result and visualization of mass spectrum.

Qiao Y, Zhang H, Bu D, Sun S.

BMC Bioinformatics. 2011 Jun 15;12:234. doi: 10.1186/1471-2105-12-234.

PMID:
21672262
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Rapid identification of protein biomarkers of Escherichia coli O157:H7 by matrix-assisted laser desorption ionization-time-of-flight-time-of-flight mass spectrometry and top-down proteomics.

Fagerquist CK, Garbus BR, Miller WG, Williams KE, Yee E, Bates AH, Boyle S, Harden LA, Cooley MB, Mandrell RE.

Anal Chem. 2010 Apr 1;82(7):2717-25. doi: 10.1021/ac902455d.

PMID:
20232878
[PubMed - indexed for MEDLINE]
20.

An algorithm for identifying multiply modified endogenous proteins using both full-scan and high-resolution tandem mass spectrometric data.

Mazur MT, Fyhr R.

Rapid Commun Mass Spectrom. 2011 Dec 15;25(23):3617-26. doi: 10.1002/rcm.5257.

PMID:
22095511
[PubMed - indexed for MEDLINE]

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