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Items: 1 to 20 of 254

1.

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
2.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

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

PLoS One. 2015 Apr 30;10(4):e0125108. doi: 10.1371/journal.pone.0125108. eCollection 2015.

3.

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
4.

OpenMS and TOPP: open source software for LC-MS data analysis.

Reinert K, Kohlbacher O.

Methods Mol Biol. 2010;604:201-11. doi: 10.1007/978-1-60761-444-9_14.

PMID:
20013373
5.

ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.

Falkner JA, Falkner JW, Andrews PC.

Bioinformatics. 2007 Jan 15;23(2):262-3. Epub 2006 Nov 22.

PMID:
17121776
6.

OpenMS and TOPP: open source software for LC-MS data analysis.

Bertsch A, Gröpl C, Reinert K, Kohlbacher O.

Methods Mol Biol. 2011;696:353-67. doi: 10.1007/978-1-60761-987-1_23.

PMID:
21063960
7.

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.

8.

TOPP--the OpenMS proteomics pipeline.

Kohlbacher O, Reinert K, Gröpl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M.

Bioinformatics. 2007 Jan 15;23(2):e191-7.

PMID:
17237091
9.

A collection of open source applications for mass spectrometry data mining.

Gallardo Ó, Ovelleiro D, Gay M, Carrascal M, Abian J.

Proteomics. 2014 Oct;14(20):2275-9. doi: 10.1002/pmic.201400124. Epub 2014 Sep 5.

PMID:
25055762
10.

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

Röst HL, Rosenberger G, Aebersold R, Malmström L.

Bioinformatics. 2015 Jul 15;31(14):2415-7. doi: 10.1093/bioinformatics/btv152. Epub 2015 Mar 18.

11.

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
12.

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.

13.

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows.

Kiefer P, Schmitt U, Vorholt JA.

Bioinformatics. 2013 Apr 1;29(7):963-4. doi: 10.1093/bioinformatics/btt080. Epub 2013 Feb 15.

14.

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.

Proteomics. 2012 Mar;12(6):795-8. doi: 10.1002/pmic.201100578.

15.

OpenMS - an open-source software framework for mass spectrometry.

Sturm M, Bertsch A, Gröpl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O.

BMC Bioinformatics. 2008 Mar 26;9:163. doi: 10.1186/1471-2105-9-163.

16.

TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data.

Junker J, Bielow C, Bertsch A, Sturm M, Reinert K, Kohlbacher O.

J Proteome Res. 2012 Jul 6;11(7):3914-20. doi: 10.1021/pr300187f. Epub 2012 May 24.

PMID:
22583024
17.

p3d--Python module for structural bioinformatics.

Fufezan C, Specht M.

BMC Bioinformatics. 2009 Aug 21;10:258. doi: 10.1186/1471-2105-10-258.

18.

OpenMS: a flexible open-source software platform for mass spectrometry data analysis.

Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O.

Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.

PMID:
27575624
19.

psims - A Declarative Writer for mzML and mzIdentML for Python.

Klein J, Zaia J.

Mol Cell Proteomics. 2019 Mar;18(3):571-575. doi: 10.1074/mcp.RP118.001070. Epub 2018 Dec 18.

PMID:
30563850
20.

mMass 3: a cross-platform software environment for precise analysis of mass spectrometric data.

Strohalm M, Kavan D, Novák P, Volný M, Havlícek V.

Anal Chem. 2010 Jun 1;82(11):4648-51. doi: 10.1021/ac100818g.

PMID:
20465224

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