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Results: 1 to 20 of 123

1.

ProteoStats--a library for estimating false discovery rates in proteomics pipelines.

Yadav AK, Kadimi PK, Kumar D, Dash D.

Bioinformatics. 2013 Nov 1;29(21):2799-800. doi: 10.1093/bioinformatics/btt490. Epub 2013 Aug 20.

PMID:
23962616
[PubMed - indexed for MEDLINE]
2.

Decoy-free protein-level false discovery rate estimation.

Teng B, Huang T, He Z.

Bioinformatics. 2014 Mar 1;30(5):675-81. doi: 10.1093/bioinformatics/btt431. Epub 2013 Aug 6.

PMID:
23926225
[PubMed - indexed for MEDLINE]
3.

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
4.

An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates.

Ahrné E, Ohta Y, Nikitin F, Scherl A, Lisacek F, Müller M.

Proteomics. 2011 Oct;11(20):4085-95. doi: 10.1002/pmic.201000665. Epub 2011 Sep 7.

PMID:
21898822
[PubMed - indexed for MEDLINE]
5.

Target-decoy approach and false discovery rate: when things may go wrong.

Gupta N, Bandeira N, Keich U, Pevzner PA.

J Am Soc Mass Spectrom. 2011 Jul;22(7):1111-20. doi: 10.1007/s13361-011-0139-3. Epub 2011 May 5.

PMID:
21953092
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics.

Lam H, Deutsch EW, Aebersold R.

J Proteome Res. 2010 Jan;9(1):605-10. doi: 10.1021/pr900947u.

PMID:
19916561
[PubMed - indexed for MEDLINE]
7.

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.

Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.

Mol Cell Proteomics. 2011 Dec;10(12):M111.007690. doi: 10.1074/mcp.M111.007690. Epub 2011 Aug 29.

PMID:
21876204
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Decoy methods for assessing false positives and false discovery rates in shotgun proteomics.

Wang G, Wu WW, Zhang Z, Masilamani S, Shen RF.

Anal Chem. 2009 Jan 1;81(1):146-59. doi: 10.1021/ac801664q.

PMID:
19061407
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Two-dimensional target decoy strategy for shotgun proteomics.

Bern MW, Kil YJ.

J Proteome Res. 2011 Dec 2;10(12):5296-301. doi: 10.1021/pr200780j. Epub 2011 Nov 7.

PMID:
22010998
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

False discovery rate estimation for cross-linked peptides identified by mass spectrometry.

Walzthoeni T, Claassen M, Leitner A, Herzog F, Bohn S, Förster F, Beck M, Aebersold R.

Nat Methods. 2012 Sep;9(9):901-3. doi: 10.1038/nmeth.2103. Epub 2012 Jul 8.

PMID:
22772729
[PubMed - indexed for MEDLINE]
11.

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
[PubMed - indexed for MEDLINE]
12.

Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications.

Du X, Yang F, Manes NP, Stenoien DL, Monroe ME, Adkins JN, States DJ, Purvine SO, Camp DG 2nd, Smith RD.

J Proteome Res. 2008 Jun;7(6):2195-203. doi: 10.1021/pr070510t. Epub 2008 Apr 19.

PMID:
18422353
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines.

Jones AR, Siepen JA, Hubbard SJ, Paton NW.

Proteomics. 2009 Mar;9(5):1220-9. doi: 10.1002/pmic.200800473.

PMID:
19253293
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A graph-based approach for designing extensible pipelines.

Rodrigues MR, Magalhães WC, Machado M, Tarazona-Santos E.

BMC Bioinformatics. 2012 Jul 12;13:163. doi: 10.1186/1471-2105-13-163.

PMID:
22788675
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

BuildSummary: using a group-based approach to improve the sensitivity of peptide/protein identification in shotgun proteomics.

Sheng Q, Dai J, Wu Y, Tang H, Zeng R.

J Proteome Res. 2012 Mar 2;11(3):1494-502. doi: 10.1021/pr200194p. Epub 2012 Feb 8.

PMID:
22217156
[PubMed - indexed for MEDLINE]
16.

False discovery rates in spectral identification.

Jeong K, Kim S, Bandeira N.

BMC Bioinformatics. 2012;13 Suppl 16:S2. doi: 10.1186/1471-2105-13-S16-S2. Epub 2012 Nov 5.

PMID:
23176207
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline.

Dowsey AW, Dunn MJ, Yang GZ.

Bioinformatics. 2008 Apr 1;24(7):950-7. doi: 10.1093/bioinformatics/btn059. Epub 2008 Feb 28.

PMID:
18310057
[PubMed - indexed for MEDLINE]
Free Article
18.

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.

Choi H, Nesvizhskii AI.

J Proteome Res. 2008 Jan;7(1):254-65. Epub 2007 Dec 27.

PMID:
18159924
[PubMed - indexed for MEDLINE]
19.

Empirical approach to false discovery rate estimation in shotgun proteomics.

Goloborodko AA, Mayerhofer C, Zubarev AR, Tarasova IA, Gorshkov AV, Zubarev RA, Gorshkov MV.

Rapid Commun Mass Spectrom. 2010 Feb;24(4):454-62. doi: 10.1002/rcm.4417.

PMID:
20069687
[PubMed - indexed for MEDLINE]
20.

Optimization of filtering criterion for SEQUEST database searching to improve proteome coverage in shotgun proteomics.

Jiang X, Jiang X, Han G, Ye M, Zou H.

BMC Bioinformatics. 2007 Aug 31;8:323.

PMID:
17761002
[PubMed - indexed for MEDLINE]
Free PMC Article

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