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  LFQProfiler and RNPxl: Open-source tools for label-free quantification and protein-RNA cross-linking integrated into Proteome Discoverer.

Veit, J., Sachsenberg, T., Chernev, A., Aichler, F., Urlaub, H., & Kohlbacher, O. (2016). LFQProfiler and RNPxl: Open-source tools for label-free quantification and protein-RNA cross-linking integrated into Proteome Discoverer. Journal of Proteome Research, 15(9), 3441-3448. doi:10.1021/acs.jproteome.6b00407.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-002B-413A-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002D-28C7-7
Genre: Journal Article

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2339502.pdf (Publisher version), 4MB
 
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 Creators:
Veit, J., Author
Sachsenberg, T., Author
Chernev, A., Author
Aichler, F., Author
Urlaub, H.1, Author              
Kohlbacher, O., Author
Affiliations:
1Research Group of Bioanalytical Mass Spectrometry, MPI for biophysical chemistry, Max Planck Society, ou_578613              

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Free keywords: Computational; Analysis; Workflow; Nodes; Open-source software
 Abstract: Modern mass spectrometry setups used in today's proteomics studies generate vast amounts of raw data, calling for highly efficient data processing and analysis tools. Software for analyzing these data is either monolithic (easy to use, but sometimes too rigid) or workflow-driven (easy to customize, but sometimes complex). Thermo Proteome Discoverer (PD) is a powerful software for workflow-driven data analysis in proteomics which, in our eyes, achieves a good trade-off between flexibility and usability. Here, we present two open-source plugins for PD providing additional functionality: LFQProfiler for label-free quantification of peptides and proteins, and RNPxl for UV-induced peptide-RNA cross-linking data analysis. LFQProfiler interacts with existing PD nodes for peptide identification and validation and takes care of the entire quantitative part of the workflow. We show that it performs at least on par with other state-of-the-art software solutions for label-free quantification in a recently published benchmark ( Ramus, C.; J. Proteomics 2016 , 132 , 51 - 62 ). The second workflow, RNPxl, represents the first software solution to date for identification of peptide-RNA cross-links including automatic localization of the cross-links at amino acid resolution and localization scoring. It comes with a customized integrated cross-link fragment spectrum viewer for convenient manual inspection and validation of the results.

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Language(s): eng - English
 Dates: 2016-08-012016-09-02
 Publication Status: Published in print
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 Rev. Method: Peer
 Identifiers: DOI: 10.1021/acs.jproteome.6b00407
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Title: Journal of Proteome Research
Source Genre: Journal
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Pages: - Volume / Issue: 15 (9) Sequence Number: - Start / End Page: 3441 - 3448 Identifier: -