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Items: 1 to 20 of 87

1.
3.

An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis.

Kapp EA, Schütz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS, Simpson RJ.

Proteomics. 2005 Aug;5(13):3475-90.

PMID:
16047398
4.

Maximizing the sensitivity and reliability of peptide identification in large-scale proteomic experiments by harnessing multiple search engines.

Yu W, Taylor JA, Davis MT, Bonilla LE, Lee KA, Auger PL, Farnsworth CC, Welcher AA, Patterson SD.

Proteomics. 2010 Mar;10(6):1172-89. doi: 10.1002/pmic.200900074.

PMID:
20101609
5.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2016 Aug 4. pii: S1874-3919(16)30344-X. doi: 10.1016/j.jprot.2016.08.002. [Epub ahead of print]

PMID:
27498275
6.

Algorithms for database-dependent search of MS/MS data.

Matthiesen R.

Methods Mol Biol. 2013;1007:119-38. doi: 10.1007/978-1-62703-392-3_5.

PMID:
23666724
7.

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.

8.

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.

9.

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
10.

Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides.

Heller M, Ye M, Michel PE, Morier P, Stalder D, Jünger MA, Aebersold R, Reymond F, Rossier JS.

J Proteome Res. 2005 Nov-Dec;4(6):2273-82.

PMID:
16335976
11.

Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy.

Balgley BM, Laudeman T, Yang L, Song T, Lee CS.

Mol Cell Proteomics. 2007 Sep;6(9):1599-608. Epub 2007 May 28.

12.

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O.

J Proteome Res. 2011 Aug 5;10(8):3332-43. doi: 10.1021/pr2002879. Epub 2011 Jun 23.

PMID:
21644507
13.

General framework for developing and evaluating database scoring algorithms using the TANDEM search engine.

MacLean B, Eng JK, Beavis RC, McIntosh M.

Bioinformatics. 2006 Nov 15;22(22):2830-2. Epub 2006 Jul 28.

14.

Overview of tandem mass spectrometry (MS/MS) database search algorithms.

Kapp E, Schütz F.

Curr Protoc Protein Sci. 2007 Aug;Chapter 25:Unit25.2. doi: 10.1002/0471140864.ps2502s49. Review.

PMID:
18429324
15.

Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold.

Brosch M, Swamy S, Hubbard T, Choudhary J.

Mol Cell Proteomics. 2008 May;7(5):962-70. doi: 10.1074/mcp.M700293-MCP200. Epub 2008 Jan 23.

16.
17.

The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search.

Kim S, Mischerikow N, Bandeira N, Navarro JD, Wich L, Mohammed S, Heck AJ, Pevzner PA.

Mol Cell Proteomics. 2010 Dec;9(12):2840-52. doi: 10.1074/mcp.M110.003731. Epub 2010 Sep 9.

18.

Practical and Efficient Searching in Proteomics: A Cross Engine Comparison.

Paulo JA.

Webmedcentral. 2013 Oct 1;4(10). pii: WMCPLS0052.

19.

Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments.

Kandasamy K, Pandey A, Molina H.

Anal Chem. 2009 Sep 1;81(17):7170-80. doi: 10.1021/ac9006107.

PMID:
19639959
20.

Improving software performance for peptide electron transfer dissociation data analysis by implementation of charge state- and sequence-dependent scoring.

Baker PR, Medzihradszky KF, Chalkley RJ.

Mol Cell Proteomics. 2010 Sep;9(9):1795-803. doi: 10.1074/mcp.M110.000422. Epub 2010 May 31.

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