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Current controlled vocabularies are insufficient to uniquely map molecular entities to mass spectrometry signal.

Smith R, Taylor RM, Prince JT.

BMC Bioinformatics. 2015;16 Suppl 7:S2. doi: 10.1186/1471-2105-16-S7-S2. Epub 2015 Apr 23.


Mono-isotope Prediction for Mass Spectra Using Bayes Network.

Li H, Liu C, Rwebangira MR, Burge L.

Tsinghua Sci Technol. 2014 Dec 1;19(6):617-623.


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.


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.


Quantitative proteomic analysis of hepatocyte-secreted extracellular vesicles reveals candidate markers for liver toxicity.

Rodríguez-Suárez E, Gonzalez E, Hughes C, Conde-Vancells J, Rudella A, Royo F, Palomo L, Elortza F, Lu SC, Mato JM, Vissers JP, Falcón-Pérez JM.

J Proteomics. 2014 May 30;103:227-40. doi: 10.1016/j.jprot.2014.04.008. Epub 2014 Apr 18.


A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.

Benjamin AM, Thompson JW, Soderblom EJ, Geromanos SJ, Henao R, Kraus VB, Moseley MA, Lucas JE.

BMC Bioinformatics. 2013 Dec 16;14:364. doi: 10.1186/1471-2105-14-364.


Analyzing LC-MS/MS data by spectral count and ion abundance: two case studies.

Milac TI, Randolph TW, Wang P.

Stat Interface. 2012;5(1):75-87.


A blood-based proteomic classifier for the molecular characterization of pulmonary nodules.

Li XJ, Hayward C, Fong PY, Dominguez M, Hunsucker SW, Lee LW, McLean M, Law S, Butler H, Schirm M, Gingras O, Lamontagne J, Allard R, Chelsky D, Price ND, Lam S, Massion PP, Pass H, Rom WN, Vachani A, Fang KC, Hood L, Kearney P.

Sci Transl Med. 2013 Oct 16;5(207):207ra142. doi: 10.1126/scitranslmed.3007013.


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.


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.


xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

Uppal K, Soltow QA, Strobel FH, Pittard WS, Gernert KM, Yu T, Jones DP.

BMC Bioinformatics. 2013 Jan 16;14:15. doi: 10.1186/1471-2105-14-15.


File formats commonly used in mass spectrometry proteomics.

Deutsch EW.

Mol Cell Proteomics. 2012 Dec;11(12):1612-21. doi: 10.1074/mcp.R112.019695. Epub 2012 Sep 6.


Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics.

Peterson AC, Russell JD, Bailey DJ, Westphall MS, Coon JJ.

Mol Cell Proteomics. 2012 Nov;11(11):1475-88. doi: 10.1074/mcp.O112.020131. Epub 2012 Aug 3.


A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.

Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR.

OMICS. 2012 Sep;16(9):431-42. doi: 10.1089/omi.2012.0022. Epub 2012 Jul 17.


msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies.

Hoekman B, Breitling R, Suits F, Bischoff R, Horvatovich P.

Mol Cell Proteomics. 2012 Jun;11(6):M111.015974. doi: 10.1074/mcp.M111.015974. Epub 2012 Feb 7.


Features-based deisotoping method for tandem mass spectra.

Yuan Z, Shi J, Lin W, Chen B, Wu FX.

Adv Bioinformatics. 2011;2011:210805. doi: 10.1155/2011/210805. Epub 2012 Jan 4.


BPDA2d--a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry.

Sun Y, Zhang J, Braga-Neto U, Dougherty ER.

Bioinformatics. 2012 Feb 15;28(4):564-72. doi: 10.1093/bioinformatics/btr675. Epub 2011 Dec 6.


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.


Bioinformatics tools for cancer metabolomics.

Blekherman G, Laubenbacher R, Cortes DF, Mendes P, Torti FM, Akman S, Torti SV, Shulaev V.

Metabolomics. 2011 Sep;7(3):329-343. Epub 2011 Jan 12.

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