Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats.

J A Falkner1, J W Falkner, P C Andrews

  • 1Department of Biochemistry, Program in Bioinformatics, Ann Arbor, MI 48109, USA. jfalkner@umich.edu

Bioinformatics (Oxford, England)
|November 24, 2006
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Selective collision-induced fragmentation of ortho-hydroxybenzyl-aminated lysyl-containing tryptic peptides.

Rapid communications in mass spectrometry : RCM·2013
Same author

Substituent effects on the gas-phase fragmentation reactions of protonated peptides containing benzylamine-derivatized lysyl residues.

Rapid communications in mass spectrometry : RCM·2012
Same author

Mass spectrometry of proteins directly from polyacrylamide gels.

Analytical chemistry·2011
Same author

Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques.

Journal of bacteriology·2007
Same author

ProteomeCommons.org JAF: reference information and tools for proteomics.

Bioinformatics (Oxford, England)·2006
Same author

Phosphopeptide derivatization signatures to identify serine and threonine phosphorylated peptides by mass spectrometry.

Analytical chemistry·2002
Same journal

Probabilistic RNA designability via interpretable ensemble approximation and dynamic decomposition.

Bioinformatics (Oxford, England)·2026
Same journal

Quantifying domain-specific relevance of computational biology Wikipedia articles using TF-IDF and cosine similarity.

Bioinformatics (Oxford, England)·2026
Same journal

GATSBI: improving context-aware protein embeddings through biologically motivated data splits.

Bioinformatics (Oxford, England)·2026
Same journal

BiMba: using Vision Mamba to predict protein sites that bind other proteins.

Bioinformatics (Oxford, England)·2026
Same journal

ProMeta: a meta-learning framework for robust disease diagnosis and prediction from plasma proteomics.

Bioinformatics (Oxford, England)·2026
Same journal

Is a Win-Win possible? Achieving pareto-optimal privacy-utility balance in fine-tuned genome language model embeddings against embedding reconstruction attacks.

Bioinformatics (Oxford, England)·2026
See all related articles

The ProteomeCommons.org Input and Output (IO) Framework simplifies proteomics data analysis by enabling seamless reading and writing of diverse mass spectrometry file formats. This open-source tool supports batch processing and research needs.

Area of Science:

  • Proteomics
  • Computational Biology
  • Bioinformatics

Background:

  • Effective utilization of mass spectrometry data is hindered by the complexity of various file formats.
  • Existing vendor-specific libraries and neutral formats (e.g., mzXML, mzData) present challenges for data extraction and batch processing.
  • Accessing and processing raw mass spectrometry data requires robust solutions for diverse experimental workflows.

Purpose of the Study:

  • To introduce the Proteome Commons.org Input and Output (IO) Framework, a novel solution for abstractly representing and managing mass spectrometry data.
  • To provide a unified framework that simplifies the handling of numerous proteomics file formats, including proprietary and legacy types.
  • To facilitate easier data extraction and preparation for downstream analysis, batch processing, and fundamental research.

Related Experiment Videos

Main Methods:

  • Development of a public, open-source, and free-to-use framework for mass spectrometry data.
  • Implementation of an abstraction layer to represent mass spectrometry data, accommodating various file formats.
  • Creation of an online tool for non-programmers and a set of libraries for developers to facilitate file format conversion.

Main Results:

  • The IO Framework supports a wide array of mass spectrometry data formats, including current, legacy, and proprietary types.
  • The framework enables efficient extraction of raw data files suitable for batch processing and research.
  • Both a user-friendly online tool and developer libraries are provided for broad accessibility and application.

Conclusions:

  • The Proteome Commons.org IO Framework significantly enhances the usability of proteomics mass spectrometry data.
  • It addresses the critical need for simplified data handling across diverse file formats in proteomics research.
  • The framework promotes wider accessibility and application of mass spectrometry data through its open-source nature and versatile tools.