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Items: 1 to 20 of 109

1.

MetiTree: a web application to organize and process high-resolution multi-stage mass spectrometry metabolomics data.

Rojas-Chertó M, van Vliet M, Peironcely JE, van Doorn R, Kooyman M, te Beek T, van Driel MA, Hankemeier T, Reijmers T.

Bioinformatics. 2012 Oct 15;28(20):2707-9. doi: 10.1093/bioinformatics/bts486. Epub 2012 Jul 31.

2.

Automated pipeline for de novo metabolite identification using mass-spectrometry-based metabolomics.

Peironcely JE, Rojas-Chertó M, Tas A, Vreeken R, Reijmers T, Coulier L, Hankemeier T.

Anal Chem. 2013 Apr 2;85(7):3576-83. doi: 10.1021/ac303218u. Epub 2013 Mar 21.

3.

Metabolite identification using automated comparison of high-resolution multistage mass spectral trees.

Rojas-Cherto M, Peironcely JE, Kasper PT, van der Hooft JJ, de Vos RC, Vreeken R, Hankemeier T, Reijmers T.

Anal Chem. 2012 Jul 3;84(13):5524-34. doi: 10.1021/ac2034216. Epub 2012 Jun 22.

PMID:
22612383
4.

Substructure-based annotation of high-resolution multistage MS(n) spectral trees.

Ridder L, van der Hooft JJ, Verhoeven S, de Vos RC, van Schaik R, Vervoort J.

Rapid Commun Mass Spectrom. 2012 Oct 30;26(20):2461-71. doi: 10.1002/rcm.6364.

PMID:
22976213
5.

Polyphenol identification based on systematic and robust high-resolution accurate mass spectrometry fragmentation.

van der Hooft JJ, Vervoort J, Bino RJ, Beekwilder J, de Vos RC.

Anal Chem. 2011 Jan 1;83(1):409-16. doi: 10.1021/ac102546x. Epub 2010 Dec 9.

PMID:
21141940
6.
7.

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

Carroll AJ, Badger MR, Harvey Millar A.

BMC Bioinformatics. 2010 Jul 14;11:376. doi: 10.1186/1471-2105-11-376.

8.

TOPPView: an open-source viewer for mass spectrometry data.

Sturm M, Kohlbacher O.

J Proteome Res. 2009 Jul;8(7):3760-3. doi: 10.1021/pr900171m.

PMID:
19425593
9.

Elemental composition determination based on MS(n).

Rojas-Chertó M, Kasper PT, Willighagen EL, Vreeken RJ, Hankemeier T, Reijmers TH.

Bioinformatics. 2011 Sep 1;27(17):2376-83. doi: 10.1093/bioinformatics/btr409. Epub 2011 Jul 14.

PMID:
21757467
10.

MeltDB: a software platform for the analysis and integration of metabolomics experiment data.

Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A.

Bioinformatics. 2008 Dec 1;24(23):2726-32. doi: 10.1093/bioinformatics/btn452. Epub 2008 Sep 2.

PMID:
18765459
11.

mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics.

Thielen B, Heinen S, Schomburg D.

BMC Bioinformatics. 2009 Jul 22;10:229. doi: 10.1186/1471-2105-10-229.

12.

Web-based resources for mass-spectrometry-based metabolomics: a user's guide.

Tohge T, Fernie AR.

Phytochemistry. 2009 Mar;70(4):450-6. doi: 10.1016/j.phytochem.2009.02.004. Epub 2009 Mar 13. Review.

PMID:
19285697
13.

A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data.

Ahmad I, Suits F, Hoekman B, Swertz MA, Byelas H, Dijkstra M, Hooft R, Katsubo D, van Breukelen B, Bischoff R, Horvatovich P.

Bioinformatics. 2011 Apr 15;27(8):1176-8. doi: 10.1093/bioinformatics/btr094. Epub 2011 Feb 23.

PMID:
21349866
14.

TICL--a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics.

Antonov AV, Dietmann S, Wong P, Mewes HW.

FEBS J. 2009 Apr;276(7):2084-94. doi: 10.1111/j.1742-4658.2009.06943.x.

15.

MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation.

Biswas A, Mynampati KC, Umashankar S, Reuben S, Parab G, Rao R, Kannan VS, Swarup S.

Bioinformatics. 2010 Oct 15;26(20):2639-40. doi: 10.1093/bioinformatics/btq436. Epub 2010 Aug 11.

PMID:
20702401
16.

Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap.

Scheltema RA, Kamleh A, Wildridge D, Ebikeme C, Watson DG, Barrett MP, Jansen RC, Breitling R.

Proteomics. 2008 Nov;8(22):4647-56. doi: 10.1002/pmic.200800314.

PMID:
18937253
17.

MetaboAnalyst: a web server for metabolomic data analysis and interpretation.

Xia J, Psychogios N, Young N, Wishart DS.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W652-60. doi: 10.1093/nar/gkp356. Epub 2009 May 8.

18.

HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries.

Zhou J, Weber RJ, Allwood JW, Mistrik R, Zhu Z, Ji Z, Chen S, Dunn WB, He S, Viant MR.

Bioinformatics. 2014 Feb 15;30(4):581-3. doi: 10.1093/bioinformatics/btt711. Epub 2013 Dec 11.

19.

New bioinformatics resources for metabolomics.

Markley JL, Anderson ME, Cui Q, Eghbalnia HR, Lewis IA, Hegeman AD, Li J, Schulte CF, Sussman MR, Westler WM, Ulrich EL, Zolnai Z.

Pac Symp Biocomput. 2007:157-68.

20.

USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression.

van Kampen AH, van Schaik BD, Pauws E, Michiels EM, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JA, Baas F, van der Mee M.

Bioinformatics. 2000 Oct;16(10):899-905.

PMID:
11120679

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