ArticleJournal of proteome research2020
ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion.
Article in Journal of proteome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 2 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
128 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- An AI-Ready Phosphorylation Meta-Analysis forJournal of proteome research · 2026Pooled it
- Mass Spectral Feature Analysis of Ubiquitylated Peptides Provides Insights into Probing the Dark Ubiquitylome.Journal of the American Society for Mass Spectrometry · 2024Pooled it
- Switches in alternatively spliced isoforms impact protein and drug interactions in melanoma, ovarian cancer, and acute myeloid leukemia.British journal of cancer · 2026Article
- Micro- and Macro-Heterogeneity of N-Glycoproteome Remodeling in Endoplasmic Reticulum Stress.Molecular & cellular proteomics : MCP · 2026Article
- Characterization of aliA and aliB deletion mutants reveals a dominant role of AliA in Haloferax volcanii lipoprotein lipidation.The Journal of biological chemistry · 2026Article
- Air-Mass Influence, Radiation, and Melt-Season Dynamics Jointly Shape Dissolved Organic Matter Composition and Radiocarbon Age in Glacier Outflows on the Tibetan Plateau.Environmental science & technology · 2026Article
- Article
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- Unlocking ferroptosis heterogeneity: ATF4 versus SREBF transcriptional programs.Cell death discovery · 2026Article
- Self-assembling proteins compose the chemically resistant shell biomaterial of planktonic tintinnid ciliates.Nature communications · 2026Article
- Uncovering functional variants using a high-efficiency PE3-based screening platform.Science advances · 2026Article
- Polyketide synthase-based controlled synthesis of polycyclopropanated fuel molecules.Nature communications · 2026Article
- A Landscape Analysis of Human SUMOylation.Molecular & cellular proteomics : MCP · 2026Article
- Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.Microbiome · 2026Article
- TheJournal of proteome research · 2026Article
- PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR.Proteomes · 2026Article
- Integrated proteomics, molecular dynamics, andRSC advances · 2026Article
- The ProteomeXchange consortium in 2026: making proteomics data FAIR.Nucleic acids research · 2026Article
- Identification of Peptides Encoded by Small Open Reading Frames in Microalgae by Mass Spectrometry.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Core rumen microbes are functional generalists that sustain host metabolism and gut ecosystem function.Nature ecology & evolution · 2026Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed 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 present ThermoRawFileParser, an open-source, cross-platform 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 package and BioContainers container around ThermoRawFileParser. In addition, we implemented a user-friendly interface (ThermoRawFileParserGUI) for those users not familiar with command-line tools. Finally, we performed a benchmark of ThermoRawFileParser and msconvert to verify that the converted mzML files contain reliable quantitative results.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.