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https://github.com/compomics/thermo-msf-parser

Parser and viewer for thermo msf files.

https://github.com/compomics/thermo-msf-parser

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
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    .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
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    Academic publication links
    Links to: acs.org
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    Academic email domains
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords

bioinformatics proteomics
Last synced: 5 months ago · JSON representation

Repository

Parser and viewer for thermo msf files.

Basic Info
  • Host: GitHub
  • Owner: CompOmics
  • Language: Java
  • Default Branch: master
  • Homepage:
  • Size: 42 MB
Statistics
  • Stars: 3
  • Watchers: 17
  • Forks: 4
  • Open Issues: 4
  • Releases: 0
Topics
bioinformatics proteomics
Created almost 11 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.md

Thermo MSF Parser

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Project Description

Thermo ProteomeDiscoverer integrates both the peptide identification and quantification steps in peptide centric proteomics into a single workflow. This makes it one of the preferred programs to analyze proteomics data from Thermo mass spectrometers. The results of the ProteomeDiscoverer workflow are stored in MSF files. Here, we present a Java library to parse and visualize these MSF files.

Supported MSF Versions: Note that we only support MSF files from ProteomeDiscoverer version 1.2, 1.3 and 1.4. We are not planning to invest development time in supporting older versions, but will however, try to ensure forward compatibility as new versions of ProteomeDiscoverer become available.

Citation

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Downloads

| Download | Version | Release info | | :--: |:--:| :--:| | download | 2.0.5 - All platforms | Release notes |

Example Dataset

Example Dataset 1, click on raw to download.

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Usage

See the wiki for additional information on how to use Thermo MSF Parser.

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Related Projects

The Thermo MSF viewer makes use of compomics-utilities and JSparklines to visualize every bit of information found in the msf files.

Similar parsers for OMSSA and X!Tandem results files are also available, see OMSSA Parser and XTandem Parser.

You might also find some of the following projects interesting: Peptizer, dbtoolkit, ms-lims, Rover and PeptideShaker.

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Project Support

The Thermo MSF Parser project is grateful for the support by:

| Compomics | VIB | Ghent University| |:--:|:--:|:--:| | compomics | vib | ugent |

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| IntelliJ | Netbeans | Java | Maven | |:--:|:--:|:--:|:--:| | intellij | netbeans | java | maven |

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Owner

  • Name: Computational Omics and Systems Biology Group
  • Login: CompOmics
  • Kind: organization
  • Email: compomics.list@gmail.com

The CompOmics group, headed by Prof. Dr. Lennart Martens, specializes in the management, analysis and integration of high-throughput Omics data.

GitHub Events

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Dependencies

pom.xml maven
  • com.compomics:utilities 3.15.36
  • log4j:log4j 1.2.17
  • junit:junit 4.11 test
thermo_msf_parser_API/pom.xml maven
  • com.compomics:utilities
  • junit:junit
  • org.apache.commons:commons-lang3 3.1
  • org.xerial:sqlite-jdbc 3.7.15-M1
  • commons-io:commons-io 2.4 test
thermo_msf_parser_GUI/pom.xml maven
  • com.compomics.thermo_msf_parser:thermo_msf_parser_API 2.0.6
  • com.compomics:utilities