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Items: 1 to 20 of 109

1.

DIANA--algorithmic improvements for analysis of data-independent acquisition MS data.

Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F.

Bioinformatics. 2015 Feb 15;31(4):555-62. doi: 10.1093/bioinformatics/btu686. Epub 2014 Oct 27.

2.

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

Goloborodko AA, Levitsky LI, Ivanov MV, Gorshkov MV.

J Am Soc Mass Spectrom. 2013 Feb;24(2):301-4. doi: 10.1007/s13361-012-0516-6. Epub 2013 Jan 5.

PMID:
23292976
3.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

Röst HL, Schmitt U, Aebersold R, Malmström L.

Proteomics. 2014 Jan;14(1):74-7. doi: 10.1002/pmic.201300246.

PMID:
24420968
4.

Improvements in Mass Spectrometry Assay Library Generation for Targeted Proteomics.

Teleman J, Hauri S, Malmström J.

J Proteome Res. 2017 Jul 7;16(7):2384-2392. doi: 10.1021/acs.jproteome.6b00928. Epub 2017 Jun 6.

PMID:
28516777
5.

specL--an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics.

Panse C, Trachsel C, Grossmann J, Schlapbach R.

Bioinformatics. 2015 Jul 1;31(13):2228-31. doi: 10.1093/bioinformatics/btv105. Epub 2015 Feb 23.

PMID:
25712692
6.

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.

Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255. Epub 2015 Jan 19.

7.

Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

Teleman J, Chawade A, Sandin M, Levander F, Malmström J.

J Proteome Res. 2016 Jul 1;15(7):2143-51. doi: 10.1021/acs.jproteome.6b00016. Epub 2016 Jun 8.

8.

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data.

Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R.

Nat Biotechnol. 2014 Mar;32(3):219-23. doi: 10.1038/nbt.2841. No abstract available.

PMID:
24727770
9.

MS2PIP: a tool for MS/MS peak intensity prediction.

Degroeve S, Martens L.

Bioinformatics. 2013 Dec 15;29(24):3199-203. doi: 10.1093/bioinformatics/btt544. Epub 2013 Sep 27.

10.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

Muth T, Rapp E, Berven FS, Barsnes H, Vaudel M.

Adv Exp Med Biol. 2016;919:217-226. Review.

PMID:
27975219
11.

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
12.

ETISEQ--an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics.

Wong JW, Schwahn AB, Downard KM.

BMC Bioinformatics. 2009 Aug 10;10:244. doi: 10.1186/1471-2105-10-244.

13.

ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity.

Xu T, Park SK, Venable JD, Wohlschlegel JA, Diedrich JK, Cociorva D, Lu B, Liao L, Hewel J, Han X, Wong CCL, Fonslow B, Delahunty C, Gao Y, Shah H, Yates JR 3rd.

J Proteomics. 2015 Nov 3;129:16-24. doi: 10.1016/j.jprot.2015.07.001. Epub 2015 Jul 11.

14.

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.

15.

ScanRanker: Quality assessment of tandem mass spectra via sequence tagging.

Ma ZQ, Chambers MC, Ham AJ, Cheek KL, Whitwell CW, Aerni HR, Schilling B, Miller AW, Caprioli RM, Tabb DL.

J Proteome Res. 2011 Jul 1;10(7):2896-904. doi: 10.1021/pr200118r. Epub 2011 Apr 26.

16.

Targeted Feature Detection for Data-Dependent Shotgun Proteomics.

Weisser H, Choudhary JS.

J Proteome Res. 2017 Aug 4;16(8):2964-2974. doi: 10.1021/acs.jproteome.7b00248. Epub 2017 Jul 19.

17.

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.

18.

IPeak: An open source tool to combine results from multiple MS/MS search engines.

Wen B, Du C, Li G, Ghali F, Jones AR, Käll L, Xu S, Zhou R, Ren Z, Feng Q, Xu X, Wang J.

Proteomics. 2015 Sep;15(17):2916-20. doi: 10.1002/pmic.201400208. Epub 2015 Aug 6.

PMID:
25951428
19.

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

Käll L, Canterbury JD, Weston J, Noble WS, MacCoss MJ.

Nat Methods. 2007 Nov;4(11):923-5. Epub 2007 Oct 21.

PMID:
17952086
20.

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.

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