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Items: 1 to 20 of 92

1.

Assigning statistical significance to proteotypic peptides via database searches.

Alves G, Ogurtsov AY, Yu YK.

J Proteomics. 2011 Feb 1;74(2):199-211. doi: 10.1016/j.jprot.2010.10.005. Epub 2010 Nov 3.

2.

The use of proteotypic peptide libraries for protein identification.

Craig R, Cortens JP, Beavis RC.

Rapid Commun Mass Spectrom. 2005;19(13):1844-50.

PMID:
15945033
3.

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
4.
5.

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

Alves G, Ogurtsov AY, Yu YK.

BMC Genomics. 2008 Oct 27;9:505. doi: 10.1186/1471-2164-9-505.

6.

Characterization of strategies for obtaining confident identifications in bottom-up proteomics measurements using hybrid FTMS instruments.

Tolmachev AV, Monroe ME, Purvine SO, Moore RJ, Jaitly N, Adkins JN, Anderson GA, Smith RD.

Anal Chem. 2008 Nov 15;80(22):8514-25. doi: 10.1021/ac801376g. Epub 2008 Oct 15.

7.
8.

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
9.

RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics.

Alves G, Ogurtsov AY, Yu YK.

PLoS One. 2010 Nov 16;5(11):e15438. doi: 10.1371/journal.pone.0015438.

10.
11.

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
12.

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.

Searle BC, Turner M, Nesvizhskii AI.

J Proteome Res. 2008 Jan;7(1):245-53. doi: 10.1021/pr070540w.

PMID:
18173222
13.
14.

Tandem Mass Spectrum Identification via Cascaded Search.

Kertesz-Farkas A, Keich U, Noble WS.

J Proteome Res. 2015 Aug 7;14(8):3027-38. doi: 10.1021/pr501173s. Epub 2015 Jun 30.

15.
17.

Analysis of the resolution limitations of peptide identification algorithms.

Colaert N, Degroeve S, Helsens K, Martens L.

J Proteome Res. 2011 Dec 2;10(12):5555-61. doi: 10.1021/pr200913a. Epub 2011 Oct 26.

PMID:
21995378
18.

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.

PMID:
20568665
19.

Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.

Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH.

J Proteomics. 2014 Aug 28;108:269-83. doi: 10.1016/j.jprot.2014.05.011. Epub 2014 May 27.

PMID:
24878426
20.

Clustering millions of tandem mass spectra.

Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA.

J Proteome Res. 2008 Jan;7(1):113-22. Epub 2007 Dec 8.

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