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

Journal of Proteome Research
Johannes JunkerOliver Kohlbacher

Abstract

Mass spectrometry coupled to high-performance liquid chromatography (HPLC-MS) is evolving more quickly than ever. A wide range of different instrument types and experimental setups are commonly used. Modern instruments acquire huge amounts of data, thus requiring tools for an efficient and automated data analysis. Most existing software for analyzing HPLC-MS data is monolithic and tailored toward a specific application. A more flexible alternative consists of pipeline-based tool kits allowing the construction of custom analysis workflows from small building blocks, e.g., the Trans Proteomics Pipeline (TPP) or The OpenMS Proteomics Pipeline (TOPP). One drawback, however, is the hurdle of setting up complex workflows using command line tools. We present TOPPAS, The OpenMS Proteomics Pipeline ASsistant, a graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction reduces to simple drag-and-drop of analysis tools and adding connections in between. Integration of external tools into these workflows is possible as well. Once workflows have been developed, they can be deployed in other workflow management systems or batch processing systems in a fully automated fashion. The implementation...Continue Reading

References

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Citations

Nov 2, 2013·Molecular & Cellular Proteomics : MCP·Erhan KenarOliver Kohlbacher
Nov 26, 2013·Biochimica Et Biophysica Acta·Chris BauerJohannes Schuchhardt
Dec 1, 2012·Expert Review of Proteomics·Marc VaudelLennart Martens
Dec 29, 2015·Journal of Proteome Research·Lukas P M KremerChristian Fufezan
Jan 6, 2016·Mass Spectrometry Reviews·Han HuJoseph Zaia
Mar 13, 2016·BMC Bioinformatics·Luis de la GarzaOliver Kohlbacher
Jan 16, 2013·Proteomics·J Alberto Medina-AunonAndrew J Jones
Sep 4, 2015·BMC Bioinformatics·Sonja HollMagnus Palmblad
Apr 10, 2013·Biochimica Et Biophysica Acta·Marianne SandinFredrik Levander
Nov 22, 2014·Journal of Proteome Research·Timo SachsenbergOliver Kohlbacher
Feb 9, 2013·Journal of Proteome Research·Hendrik WeisserLars Malmström
Oct 18, 2016·Proteomics·Wout BittremieuxKris Laukens
Oct 28, 2016·Journal of Proteome Research·Hendrik WeisserJyoti S Choudhary
Jun 1, 2017·Journal of Biotechnology·Julianus PfeufferOliver Kohlbacher
Aug 31, 2016·Nature Methods·Hannes L RöstOliver Kohlbacher
Aug 26, 2020·Nature Methods·Louis-Félix NothiasPieter C Dorrestein
May 26, 2016·Journal of Proteome Research·Johan TelemanJohan Malmström
Jan 20, 2021·Current Protein & Peptide Science·Filippo Rusconi

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