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Results: 1 to 20 of 304

1.

Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation.

Schilling B, Rardin MJ, MacLean BX, Zawadzka AM, Frewen BE, Cusack MP, Sorensen DJ, Bereman MS, Jing E, Wu CC, Verdin E, Kahn CR, Maccoss MJ, Gibson BW.

Mol Cell Proteomics. 2012 May;11(5):202-14. doi: 10.1074/mcp.M112.017707. Epub 2012 Mar 26.

PMID:
22454539
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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
3.

Exploring skyline for both MS(E) -based label-free proteomics and HRMS quantitation of small molecules.

Liu S, Chen X, Yan Z, Qin S, Xu J, Lin J, Yang C, Shui W.

Proteomics. 2014 Feb;14(2-3):169-80. doi: 10.1002/pmic.201300352. Epub 2014 Jan 6.

PMID:
24307133
[PubMed - in process]
4.

Hydroponic isotope labeling of entire plants and high-performance mass spectrometry for quantitative plant proteomics.

Bindschedler LV, Mills DJ, Cramer R.

Methods Mol Biol. 2012;893:155-73. doi: 10.1007/978-1-61779-885-6_12.

PMID:
22665301
[PubMed - indexed for MEDLINE]
5.

Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments.

Thompson AJ, Abu M, Hanger DP.

Amino Acids. 2012 Sep;43(3):1075-85. doi: 10.1007/s00726-012-1287-x. Epub 2012 Jul 22. Review.

PMID:
22821266
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
19068132
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis.

Gillet LC, Navarro P, Tate S, Röst H, Selevsek N, Reiter L, Bonner R, Aebersold R.

Mol Cell Proteomics. 2012 Jun;11(6):O111.016717. doi: 10.1074/mcp.O111.016717. Epub 2012 Jan 18.

PMID:
22261725
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Occurrence and detection of phosphopeptide isomers in large-scale phosphoproteomics experiments.

Courcelles M, Bridon G, Lemieux S, Thibault P.

J Proteome Res. 2012 Jul 6;11(7):3753-65. doi: 10.1021/pr300229m. Epub 2012 Jun 22.

PMID:
22668510
[PubMed - indexed for MEDLINE]
10.

Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.

Wang G, Wu WW, Zeng W, Chou CL, Shen RF.

J Proteome Res. 2006 May;5(5):1214-23.

PMID:
16674111
[PubMed - indexed for MEDLINE]
11.

Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification.

Vasilj A, Gentzel M, Ueberham E, Gebhardt R, Shevchenko A.

J Proteome Res. 2012 Jul 6;11(7):3680-9. doi: 10.1021/pr300147z. Epub 2012 Jun 21.

PMID:
22671763
[PubMed - indexed for MEDLINE]
12.

Mass spectrometry (LC-MS/MS) identified proteomic biosignatures of breast cancer in proximal fluid.

Whelan SA, He J, Lu M, Souda P, Saxton RE, Faull KF, Whitelegge JP, Chang HR.

J Proteome Res. 2012 Oct 5;11(10):5034-45. doi: 10.1021/pr300606e. Epub 2012 Sep 20.

PMID:
22934887
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Proteome-wide detection and quantitative analysis of irreversible cysteine oxidation using long column UPLC-pSRM.

Lee CF, Paull TT, Person MD.

J Proteome Res. 2013 Oct 4;12(10):4302-15. doi: 10.1021/pr400201d. Epub 2013 Sep 6.

PMID:
23964713
[PubMed - indexed for MEDLINE]
14.

ISPTM: an iterative search algorithm for systematic identification of post-translational modifications from complex proteome mixtures.

Huang X, Huang L, Peng H, Guru A, Xue W, Hong SY, Liu M, Sharma S, Fu K, Caprez AP, Swanson DR, Zhang Z, Ding SJ.

J Proteome Res. 2013 Sep 6;12(9):3831-42. doi: 10.1021/pr4003883. Epub 2013 Aug 6.

PMID:
23919725
[PubMed - indexed for MEDLINE]
15.

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
16.

Complementary proteomic analysis of protein complexes.

Greco TM, Miteva Y, Conlon FL, Cristea IM.

Methods Mol Biol. 2012;917:391-407. doi: 10.1007/978-1-61779-992-1_22.

PMID:
22956100
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos.

Li Z, Adams RM, Chourey K, Hurst GB, Hettich RL, Pan C.

J Proteome Res. 2012 Mar 2;11(3):1582-90. doi: 10.1021/pr200748h. Epub 2012 Feb 16.

PMID:
22188275
[PubMed - indexed for MEDLINE]
18.

MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.

Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Körner E, Rader R, Schmidt A, Mechtler K, Trajanoski Z.

BMC Bioinformatics. 2007 Jun 13;8:197.

PMID:
17567892
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Current challenges in software solutions for mass spectrometry-based quantitative proteomics.

Cappadona S, Baker PR, Cutillas PR, Heck AJ, van Breukelen B.

Amino Acids. 2012 Sep;43(3):1087-108. doi: 10.1007/s00726-012-1289-8. Epub 2012 Jul 22. Review.

PMID:
22821268
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Label-free protein quantitation using weighted spectral counting.

Vogel C, Marcotte EM.

Methods Mol Biol. 2012;893:321-41. doi: 10.1007/978-1-61779-885-6_20.

PMID:
22665309
[PubMed - indexed for MEDLINE]
Free PMC Article

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