ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

Abstract

The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analysed per experiment, as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elastic compute resources such as Linux-based cluster environments and cloud infrastructures.Unfortunately, the vast majority of cross-platform proteomics tools are not able to operate directly on the proprietary formats generated by the diverse mass spectrometers. Here, we presented ThermoRawFileParser, an open-source, crossplatform tool that converts Thermo RAW files into open file formats such as MGF and the HUPO-PSI standard file format mzML. To ensure the broadest possible availability, and to increase integration capabilities with popular workflow systems such as Galaxy or Nextflow, we have also built Conda and BioContainers containers around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools.

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

“…General workflow for the reanalysis within the ArcPP. MS raw data files were downloaded from PRIDE 14 or jPOST 15 , converted into the unified HUPO Proteomics Standards Initiative standard file format mzML 97 using the Thermo-RawFileParser (for RAW files from Thermo Scientific) 98 or msConvert (for SCIEX WIFF files, with --filter peakPicking true 1-and --filter zeroSamples removeExtra) included in ProteoWizard 99 . For all subsequent file conversions, all protein database searches, as well as all statistical post-processing (if not indicated otherwise) that were performed within the ArcPP, the Python framework Ursgal (versions 0.6.5 and 0.6.6) 29 has been used.…”

Proteomic signatures of acute oxidative stress response to paraquat in the mouse heart

“…The Thermo raw spectrum files were converted to the open source .mzML format 46 using ThermoRawFileParser v.1.2.0 47 with the options (-g -f 2). MS2 spectra were searched using SEQUEST algorithm implemented in Comet (v.2019.01 rev.4) 48 against a .fasta database Uniprot/SwissProt mus musculus database accessed on 2020-03-19 (17,033 target entries) 49 .…”

Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses

“…Raw AP-MS files were first converted to mgf files using the ThermoRawFileParser (version 1.2.0) [36] . The files were analysed using PeptideShaker software (version 1.16.42) [37] configured to use three search engines (X!Tandem, MS-GF+ and Comet) via SearchGUI (version 3.3.17) [38] .…”