A Cross-platform Toolkit for Mass Spectrometry and Proteomics

By Matthew Chambers, Brendan MacLean, Robert Burke, Dario Amodei, Daniel L. Ruderman, Steffen Neumann, Laurent Gatto, Bernd Fischer, Brian S. Pratt, Jarrett D. Egertson and 33 more. Nature Biotechnology, 2012

3,664 citations recorded by the source corpus.

Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and quantify the proteins in biological and clinical samples1, identify pathways affected by endogenous and exogenous perturbations2, and characterize protein complexes3. Despite successes, the interpretation of vast proteomics datasets remains a challenge. There have been several calls for improvements and standardization of proteomics data analysis frameworks, as well as for an application-programming interface for proteomics data access4,5. In response, we have developed the ProteoWizard Toolkit, a robust set of open-source, software libraries and applications designed to facilitate proteomics research. The libraries implement the first-ever, non-commercial, unified data access interface for proteomics, bridging field-standard open formats and all common vendor formats. In addition, diverse software classes enable rapid development of vendor-agnostic proteomics software. Additionally, ProteoWizard projects and applications, building upon the core libraries, are becoming standard tools for enabling significant proteomics inquiries.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/5e3dc1cb27afafe151d15abe0d4bde7a5d0449b0

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Citations in the corpus

Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics (2015, methodology): “The mscon-verttoolwithinthefreeandopen-sourceProteoWizard[13,14] toolkit remains the standard for converting each of the vendor formats into the Proteomics Standards Initiative (PSI; [15]) mzML format [16].”
Moyamoya disease factor RNF213 is a giant E3 ligase with a dynein-like core and a distinct ubiquitin-transfer mechanism (2020, methodology): “Fragment spectra peak lists were generated from the raw MS-data using the software MSConvert (v 3.0.9974) (Chambers et al., 2012) selecting the peak picking filter.”
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation (2024, methodology): “The spectra were first centroided and converted into mzML format using ProteoWizard ( 60 ,61 ) and uploaded to MetaboAnalyst 6.0.”
MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics (2020, neutral): “Internal Standards Dependent NOMIS [43], CCMN [44]”
MetaboLights: open data repository for metabolomics (2023, methodology): “Once users select MetaboLights LC–MS files, the MDP tool downloads, applies filters and converts the selected files to mzML format using msConvert (ProteoWizard) ( 31 ) with a predefined configuration file.”
OpenMS: a flexible open-source software platform for mass spectrometry data analysis (2016, methodology): “The OpenMS project is one of several software solutions addressing the computational challenges of MS-based proteomics, each contributing in different areas such as protein inference, peptide database search and file conversion 6,7,22,23 .”