Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform
University of Michigan · Michigan Medicine · +3 more institutions
Abstract
Liquid chromatography (LC) coupled with data-independent acquisition (DIA) mass spectrometry (MS) has been increasingly used in quantitative proteomics studies. Here, we present a fast and sensitive approach for direct peptide identification from DIA data, MSFragger-DIA, which leverages the unmatched speed of the fragment ion indexing-based search engine MSFragger. Different from most existing methods, MSFragger-DIA conducts a database search of the DIA tandem mass (MS/MS) spectra prior to spectral feature detection and peak tracing across the LC dimension. To streamline the analysis of DIA data and enable easy reproducibility, we integrate MSFragger-DIA into the FragPipe computational platform for seamless…
Citation impact
- FWCI
- 38.45
- Percentile
- 100%
- References
- 80
Authors
7Topics & keywords
- Computer science
- Proteomics
- Workflow
- Proteome
- Data acquisition
- Tandem mass spectrometry
- Profiling (computer programming)
- Mass spectrometry