TOPP - the OpenMS proteomics pipeline
By Oliver Kohlbacher, Knut Reinert, Clemens Gröpl, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Marc Sturm. Bioinform., 2007
299 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/983da7ea06c1c52c458d3756a729fb21f1614aeb
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Alexey I. Nesvizhskii
- R. Aebersold
- Eric W. Deutsch
- Zhi Sun
- Luis Mendoza
- Wanding Zhou
- David D. Shteynberg
- Jimmy K. Eng
In Spectroscopy
- Alexey I. Nesvizhskii
- Eric W. Deutsch
- R. Aebersold
- Zhi Sun
- Luis Mendoza
- David D. Shteynberg
- Jimmy K. Eng
- Rob Moritz
Citations in the corpus
- A Guided Tour of the Trans-Proteomic Pipeline (2010, background): “Many tools are available from different groups and can be strung together in custom ways, but there are only a few suites of tools that aim to provide a single environment for performing all or most steps in the workflow, including the openMS proteomics pipeline (TOPP) [5], MaxQuant [6], and Abbrevi”
- MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data (2010, methodology): “Several other software packages have been introduced for LC-MS based data processing, such as XCMS 2 [22], Trans Proteomic Pipeline [23], Trequips [24], OpenMS-TOPP [25], and ProteoWizard [26].”
- Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics (2015, methodology): “Although there are a tremendous number of individual tools for processing proteomics data [6] and some developed as pipelines [7,8], the Trans-Proteomic Pipeline (TPP; [9,10]) is the most widely used free and open-source complete suite of tools for processing shotgun proteomics data with…”
- Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients (2018, methodology): “OpenMS (Kohlbacher et al., 2007; Röst et al., 2016) was used to identify polypeptides from a sample’s polypeptide database as follows: In order to allow to control for false discovery rates, decoy sequences were added to the database.”
- OpenMS – An open-source software framework for mass spectrometry (2008, methodology): “For command line tools the TOPP base class, which implements the whole command line argument handling, is provided.”
- mzML—a Community Standard for Mass Spectrometry Data (2010, unknown): “The OpenMS Proteomics Pipeline (27).”