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Items: 1 to 20 of 218

1.

Quality assessments of peptide-spectrum matches in shotgun proteomics.

Granholm V, Käll L.

Proteomics. 2011 Mar;11(6):1086-93. doi: 10.1002/pmic.201000432. Epub 2011 Feb 7.

PMID:
21365749
2.

A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods.

Degroeve S, Colaert N, Vandekerckhove J, Gevaert K, Martens L.

Proteomics. 2011 Mar;11(6):1172-80. doi: 10.1002/pmic.201000605. Epub 2011 Feb 7.

PMID:
21298791
3.

The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides.

Beck F, Lewandrowski U, Wiltfang M, Feldmann I, Geiger J, Sickmann A, Zahedi RP.

Proteomics. 2011 Mar;11(6):1099-109. doi: 10.1002/pmic.201000562. Epub 2011 Feb 7.

PMID:
21298789
4.

Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.

Tessier D, Lollier V, Larré C, Rogniaux H.

J Proteome Res. 2016 Oct 7;15(10):3481-3488. Epub 2016 Sep 6.

PMID:
27571036
5.

A stringent approach to improve the quality of nitrotyrosine peptide identifications.

Ghesquière B, Helsens K, Vandekerckhove J, Gevaert K.

Proteomics. 2011 Mar;11(6):1094-8. doi: 10.1002/pmic.201000526. Epub 2011 Feb 7.

PMID:
21298788
6.

A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision.

Colaert N, Vandekerckhove J, Gevaert K, Martens L.

Proteomics. 2011 Mar;11(6):1110-3. doi: 10.1002/pmic.201000521. Epub 2011 Feb 7.

PMID:
21365758
7.

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.

Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM.

J Proteome Res. 2011 Jul 1;10(7):2949-58. doi: 10.1021/pr2002116. Epub 2011 Apr 29.

8.

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
9.
10.

Properties of average score distributions of SEQUEST: the probability ratio method.

Martínez-Bartolomé S, Navarro P, Martín-Maroto F, López-Ferrer D, Ramos-Fernández A, Villar M, García-Ruiz JP, Vázquez J.

Mol Cell Proteomics. 2008 Jun;7(6):1135-45. doi: 10.1074/mcp.M700239-MCP200. Epub 2008 Feb 25.

11.

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
12.

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. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
13.

RT-PSM, a real-time program for peptide-spectrum matching with statistical significance.

Wu FX, Gagné P, Droit A, Poirier GG.

Rapid Commun Mass Spectrom. 2006;20(8):1199-208.

PMID:
16541396
14.

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
15.

Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis.

Zhang X, Li Y, Shao W, Lam H.

Proteomics. 2011 Mar;11(6):1075-85. doi: 10.1002/pmic.201000492. Epub 2011 Feb 7.

PMID:
21298786
16.

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
17.

Simulating and validating proteomics data and search results.

Geromanos SJ, Hughes C, Golick D, Ciavarini S, Gorenstein MV, Richardson K, Hoyes JB, Vissers JP, Langridge JI.

Proteomics. 2011 Mar;11(6):1189-211. doi: 10.1002/pmic.201000576. Epub 2011 Feb 7.

PMID:
21298790
18.

[A novel approach for peptide identification by tandem mass spectrometry].

Sheng QH, Tang HX, Xie T, Wang LS, Ding DF.

Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003 Aug;35(8):734-40. Chinese.

19.

Elective affinities--bioinformatic analysis of proteomic mass spectrometry data.

Li X, Pizarro A, Grosser T.

Arch Physiol Biochem. 2009 Dec;115(5):311-9. doi: 10.3109/13813450903390039. Review.

PMID:
19911947
20.

Protein identification by tandem mass spectrometry and sequence database searching.

Nesvizhskii AI.

Methods Mol Biol. 2007;367:87-119. Review.

PMID:
17185772

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