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Items: 1 to 20 of 99

1.

IsoformResolver: A peptide-centric algorithm for protein inference.

Meyer-Arendt K, Old WM, Houel S, Renganathan K, Eichelberger B, Resing KA, Ahn NG.

J Proteome Res. 2011 Jul 1;10(7):3060-75. doi: 10.1021/pr200039p. Epub 2011 Jun 7.

2.

i-RUBY: a novel software for quantitative analysis of highly accurate shotgun-proteomics liquid chromatography/tandem mass spectrometry data obtained without stable-isotope labeling of proteins.

Wada K, Ogiwara A, Nagasaka K, Tanaka N, Komatsu Y.

Rapid Commun Mass Spectrom. 2011 Apr 15;25(7):960-8. doi: 10.1002/rcm.4943. Epub 2011 Mar 14.

PMID:
21416533
3.

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.

4.

Discovery of neuropeptides in the nematode Ascaris suum by database mining and tandem mass spectrometry.

Jarecki JL, Frey BL, Smith LM, Stretton AO.

J Proteome Res. 2011 Jul 1;10(7):3098-106. doi: 10.1021/pr2001176. Epub 2011 May 27.

5.

MScDB: a mass spectrometry-centric protein sequence database for proteomics.

Marx H, Lemeer S, Klaeger S, Rattei T, Kuster B.

J Proteome Res. 2013 Jun 7;12(6):2386-98. doi: 10.1021/pr400215r. Epub 2013 May 14.

PMID:
23627461
6.

Utility of characteristic QTOF MS/MS fragmentation for MHC class I peptides.

Escobar H, Reyes-Vargas E, Jensen PE, Delgado JC, Crockett DK.

J Proteome Res. 2011 May 6;10(5):2494-507. doi: 10.1021/pr101272k. Epub 2011 Mar 30.

PMID:
21413816
7.

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
8.

A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry.

Aoshima K, Takahashi K, Ikawa M, Kimura T, Fukuda M, Tanaka S, Parry HE, Fujita Y, Yoshizawa AC, Utsunomiya S, Kajihara S, Tanaka K, Oda Y.

BMC Bioinformatics. 2014 Nov 25;15:376. doi: 10.1186/s12859-014-0376-0.

9.

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.

Zhou A, Zhang F, Chen JY.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. doi: 10.1186/1471-2105-11-S6-S7.

10.

SIR: Deterministic protein inference from peptides assigned to MS data.

Matthiesen R, Prieto G, Amorim A, Aloria K, Fullaondo A, Carvalho AS, Arizmendi JM.

J Proteomics. 2012 Jul 16;75(13):4176-83. doi: 10.1016/j.jprot.2012.05.010. Epub 2012 May 14.

PMID:
22626983
11.

Protein inference using Peptide quantification patterns.

Lukasse PN, America AH.

J Proteome Res. 2014 Jul 3;13(7):3191-9. doi: 10.1021/pr401072g. Epub 2014 May 30.

PMID:
24815921
12.

The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results.

Braisted JC, Kuntumalla S, Vogel C, Marcotte EM, Rodrigues AR, Wang R, Huang ST, Ferlanti ES, Saeed AI, Fleischmann RD, Peterson SN, Pieper R.

BMC Bioinformatics. 2008 Dec 9;9:529. doi: 10.1186/1471-2105-9-529.

13.

MultiAlign: a multiple LC-MS analysis tool for targeted omics analysis.

LaMarche BL, Crowell KL, Jaitly N, Petyuk VA, Shah AR, Polpitiya AD, Sandoval JD, Kiebel GR, Monroe ME, Callister SJ, Metz TO, Anderson GA, Smith RD.

BMC Bioinformatics. 2013 Feb 12;14:49. doi: 10.1186/1471-2105-14-49.

14.

Information-dependent LC-MS/MS acquisition with exclusion lists potentially generated on-the-fly: case study using a whole cell digest of Clostridium thermocellum.

McQueen P, Spicer V, Rydzak T, Sparling R, Levin D, Wilkins JA, Krokhin O.

Proteomics. 2012 Apr;12(8):1160-9. doi: 10.1002/pmic.201100425.

PMID:
22577018
15.

PeaksPTM: Mass spectrometry-based identification of peptides with unspecified modifications.

Han X, He L, Xin L, Shan B, Ma B.

J Proteome Res. 2011 Jul 1;10(7):2930-6. doi: 10.1021/pr200153k. Epub 2011 May 24.

PMID:
21609001
16.

Assessment of MS/MS search algorithms with parent-protein profiling.

Lin MS, Cherny JJ, Fournier CT, Roth SJ, Krizanc D, Weir MP.

J Proteome Res. 2014 Apr 4;13(4):1823-32. doi: 10.1021/pr401090d. Epub 2014 Mar 7.

17.

Isoform analysis of LC-MS/MS data from multidimensional fractionation of the serum proteome.

Krasnoselsky AL, Faca VM, Pitteri SJ, Zhang Q, Hanash SM.

J Proteome Res. 2008 Jun;7(6):2546-52. doi: 10.1021/pr7007219. Epub 2008 Apr 18.

PMID:
18419151
18.

Shotgun proteomics: a relative quantitative approach using Off-Gel electrophoresis and LC-MS/MS.

Geiser L, Dayon L, Vaezzadeh AR, Hochstrasser DF.

Methods Mol Biol. 2011;681:459-72. doi: 10.1007/978-1-60761-913-0_27.

PMID:
20978983
19.

Combination of Edman degradation of peptides with liquid chromatography/mass spectrometry workflow for peptide identification in bottom-up proteomics.

Lobas AA, Verenchikov AN, Goloborodko AA, Levitsky LI, Gorshkov MV.

Rapid Commun Mass Spectrom. 2013 Feb 15;27(3):391-400. doi: 10.1002/rcm.6462.

PMID:
23280970
20.

MSSimulator: Simulation of mass spectrometry data.

Bielow C, Aiche S, Andreotti S, Reinert K.

J Proteome Res. 2011 Jul 1;10(7):2922-9. doi: 10.1021/pr200155f. Epub 2011 Apr 28.

PMID:
21526843
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