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Items: 1 to 20 of 222

1.

KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics.

Such-Sanmartín G, Sidoli S, Ventura-Espejo E, Jensen ON.

Biochem Biophys Res Commun. 2014 Mar 21;445(4):702-7. doi: 10.1016/j.bbrc.2014.01.066. Epub 2014 Jan 27.

PMID:
24480439
2.

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.

3.

Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data.

Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L.

Bioinformatics. 2009 Mar 1;25(5):682-3. doi: 10.1093/bioinformatics/btp005. Epub 2009 Jan 6.

4.

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.

5.

Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics.

Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V, Vitek O, Zhang N, Aebersold R, Watts JD.

BMC Bioinformatics. 2008 Dec 16;9:542. doi: 10.1186/1471-2105-9-542.

6.

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
7.

Precise protein quantification based on peptide quantification using iTRAQ.

Boehm AM, Pütz S, Altenhöfer D, Sickmann A, Falk M.

BMC Bioinformatics. 2007 Jun 21;8:214.

8.

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
9.

Postexperiment monoisotopic mass filtering and refinement (PE-MMR) of tandem mass spectrometric data increases accuracy of peptide identification in LC/MS/MS.

Shin B, Jung HJ, Hyung SW, Kim H, Lee D, Lee C, Yu MH, Lee SW.

Mol Cell Proteomics. 2008 Jun;7(6):1124-34. doi: 10.1074/mcp.M700419-MCP200. Epub 2008 Feb 25.

10.

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.

Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Variyath AM, Wang M, Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H, Spiegelman C, Tempst P, Liebler DC, Stein SE.

Mol Cell Proteomics. 2010 Feb;9(2):225-41. doi: 10.1074/mcp.M900223-MCP200. Epub 2009 Oct 16.

11.

LFQuant: a label-free fast quantitative analysis tool for high-resolution LC-MS/MS proteomics data.

Zhang W, Zhang J, Xu C, Li N, Liu H, Ma J, Zhu Y, Xie H.

Proteomics. 2012 Dec;12(23-24):3475-84. doi: 10.1002/pmic.201200017.

PMID:
23081734
12.

Compid: a new software tool to integrate and compare MS/MS based protein identification results from Mascot and Paragon.

Lietzén N, Natri L, Nevalainen OS, Salmi J, Nyman TA.

J Proteome Res. 2010 Dec 3;9(12):6795-800. doi: 10.1021/pr100824w. Epub 2010 Nov 11.

PMID:
20973569
13.

A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas.

Farrah T, Deutsch EW, Omenn GS, Campbell DS, Sun Z, Bletz JA, Mallick P, Katz JE, Malmström J, Ossola R, Watts JD, Lin B, Zhang H, Moritz RL, Aebersold R.

Mol Cell Proteomics. 2011 Sep;10(9):M110.006353. doi: 10.1074/mcp.M110.006353. Epub 2011 Jun 1.

14.

Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome.

Qian WJ, Liu T, Monroe ME, Strittmatter EF, Jacobs JM, Kangas LJ, Petritis K, Camp DG 2nd, Smith RD.

J Proteome Res. 2005 Jan-Feb;4(1):53-62.

PMID:
15707357
15.

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation.

Yang TH, Chang HT, Hsiao ES, Sun JL, Wang CC, Wu HY, Liao PC, Wu WS.

BMC Bioinformatics. 2014;15 Suppl 16:S10. doi: 10.1186/1471-2105-15-S16-S10. Epub 2014 Dec 8.

16.

Proteomics technologies for the global identification and quantification of proteins.

Brewis IA, Brennan P.

Adv Protein Chem Struct Biol. 2010;80:1-44. doi: 10.1016/B978-0-12-381264-3.00001-1. Review.

PMID:
21109216
17.

Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline.

Trudgian DC, Ridlova G, Fischer R, Mackeen MM, Ternette N, Acuto O, Kessler BM, Thomas B.

Proteomics. 2011 Jul;11(14):2790-7. doi: 10.1002/pmic.201000800. Epub 2011 Jun 8.

PMID:
21656681
18.

Depletion of abundant plasma proteins and limitations of plasma proteomics.

Tu C, Rudnick PA, Martinez MY, Cheek KL, Stein SE, Slebos RJ, Liebler DC.

J Proteome Res. 2010 Oct 1;9(10):4982-91. doi: 10.1021/pr100646w.

19.

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR.

Genomics Proteomics Bioinformatics. 2015 Feb;13(1):25-35. doi: 10.1016/j.gpb.2014.11.002. Epub 2015 Feb 21.

20.

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells.

Bouyssié D, Gonzalez de Peredo A, Mouton E, Albigot R, Roussel L, Ortega N, Cayrol C, Burlet-Schiltz O, Girard JP, Monsarrat B.

Mol Cell Proteomics. 2007 Sep;6(9):1621-37. Epub 2007 May 28.

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