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Statistical quality assessment and outlier detection for liquid chromatography-mass spectrometry experiments.

Schulz-Trieglaff O, Machtejevas E, Reinert K, Schlüter H, Thiemann J, Unger K.

BioData Min. 2009 Apr 7;2(1):4.PMID: 19351414 [PubMed - in process]Related articlesFree article

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements.

Lange E, Tautenhahn R, Neumann S, Gröpl C.

BMC Bioinformatics. 2008 Sep 15;9:375.PMID: 18793413 [PubMed - indexed for MEDLINE]Related articlesFree article

Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics.

Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S, Flory MR, Lee H, Watts J, Goodlett DR, Aebersold R, Paulovich A, Schwikowski B.

Mol Cell Proteomics. 2007 Oct;6(10):1741-8. Epub 2007 Jul 7.PMID: 17617667 [PubMed - indexed for MEDLINE]Related articlesFree article

LC-MSsim--a simulation software for liquid chromatography mass spectrometry data.

Schulz-Trieglaff O, Pfeifer N, Gröpl C, Kohlbacher O, Reinert K.

BMC Bioinformatics. 2008 Oct 8;9:423.PMID: 18842122 [PubMed - indexed for MEDLINE]Related articlesFree article

Quality control metrics for LC-MS feature detection tools demonstrated on Saccharomyces cerevisiae proteomic profiles.

Piening BD, Wang P, Bangur CS, Whiteaker J, Zhang H, Feng LC, Keane JF, Eng JK, Tang H, Prakash A, McIntosh MW, Paulovich A.

J Proteome Res. 2006 Jul;5(7):1527-34.PMID: 16823959 [PubMed - indexed for MEDLINE]Related articles

Time-series alignment by non-negative multiple generalized canonical correlation analysis.

Fischer B, Roth V, Buhmann JM.

BMC Bioinformatics. 2007;8 Suppl 10:S4.PMID: 18269698 [PubMed - indexed for MEDLINE]Related articlesFree article

Computational quantification of peptides from LC-MS data.

Schulz-Trieglaff O, Hussong R, Gröpl C, Leinenbach A, Hildebrandt A, Huber C, Reinert K.

J Comput Biol. 2008 Sep;15(7):685-704.PMID: 18707556 [PubMed - indexed for MEDLINE]Related articles

Technical, bioinformatical and statistical aspects of liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis-mass spectrometry (CE-MS) based clinical proteomics: a critical assessment.

Dakna M, He Z, Yu WC, Mischak H, Kolch W.

J Chromatogr B Analyt Technol Biomed Life Sci. 2009 May 1;877(13):1250-8. Epub 2008 Nov 6. Review.PMID: 19010091 [PubMed - indexed for MEDLINE]Related articles

Investigation of uremic analytes in hemodialysate and their structural elucidation from accurate mass maps generated by a multi-dimensional liquid chromatography/mass spectrometry approach.

Godfrey AR, Williams CM, Dudley E, Newton RP, Willshaw P, Mikhail A, Bastin L, Brenton AG.

Rapid Commun Mass Spectrom. 2009 Oct;23(19):3194-204.PMID: 19718779 [PubMed - indexed for MEDLINE]Related articles

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. Epub 2009 Oct 16.PMID: 19837981 [PubMed - in process]Related articles

Increased confidence in large-scale phosphoproteomics data by complementary mass spectrometric techniques and matching of phosphopeptide data sets.

Alcolea MP, Kleiner O, Cutillas PR.

J Proteome Res. 2009 Aug;8(8):3808-15.PMID: 19537829 [PubMed - indexed for MEDLINE]Related articles

Real-time evaluation of experimental variation in large-scale LC-MS/MS-based quantitative proteomics of complex samples.

Levin Y, Wang L, Ingudomnukul E, Schwarz E, Baron-Cohen S, Palotás A, Bahn S.

J Chromatogr B Analyt Technol Biomed Life Sci. 2009 May 1;877(13):1299-305. Epub 2008 Nov 13.PMID: 19056327 [PubMed - indexed for MEDLINE]Related articles

Detecting outlier samples in microarray data.

Shieh AD, Hung YS.

Stat Appl Genet Mol Biol. 2009 Jan;8(1):Article 13. Epub 2009 Feb 11.PMID: 19222380 [PubMed - indexed for MEDLINE]Related articlesFree article

A method for improving SELDI-TOF mass spectrometry data quality.

Whistler T, Rollin D, Vernon SD.

Proteome Sci. 2007 Sep 5;5:14.PMID: 17803814 [PubMed - in process]Related articlesFree article

Data processing for mass spectrometry-based metabolomics.

Katajamaa M, Oresic M.

J Chromatogr A. 2007 Jul 27;1158(1-2):318-28. Epub 2007 Apr 19. Review.PMID: 17466315 [PubMed - indexed for MEDLINE]Related articles

Global quantitative proteomic profiling through 18O-labeling in combination with MS/MS spectra analysis.

White CA, Oey N, Emili A.

J Proteome Res. 2009 Jul;8(7):3653-65.PMID: 19400582 [PubMed - indexed for MEDLINE]Related articles

Comprehensive analytical strategy for biomarker identification based on liquid chromatography coupled to mass spectrometry and new candidate confirmation tools.

Mohamed R, Varesio E, Ivosev G, Burton L, Bonner R, Hopfgartner G.

Anal Chem. 2009 Sep 15;81(18):7677-94.PMID: 19702294 [PubMed - indexed for MEDLINE]Related articles

Assembling proteomics data as a prerequisite for the analysis of large scale experiments.

Schmidt F, Schmid M, Thiede B, Pleißner KP, Böhme M, Jungblut PR.

Chem Cent J. 2009 Jan 23;3(1):2.PMID: 19166578 [PubMed - as supplied by publisher]Related articlesFree article

Robust prediction of the MASCOT score for an improved quality assessment in mass spectrometric proteomics.

Koenig T, Menze BH, Kirchner M, Monigatti F, Parker KC, Patterson T, Steen JJ, Hamprecht FA, Steen H.

J Proteome Res. 2008 Sep;7(9):3708-17. Epub 2008 Aug 16.PMID: 18707158 [PubMed - indexed for MEDLINE]Related articles

Method validation and comparison of acetonitrile and acetone extraction for the analysis of 169 pesticides in soya grain by liquid chromatography-tandem mass spectrometry.

Pizzutti IR, de Kok A, Hiemstra M, Wickert C, Prestes OD.

J Chromatogr A. 2009 May 22;1216(21):4539-52. Epub 2009 Mar 28.PMID: 19375710 [PubMed - indexed for MEDLINE]Related articles