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RAId: Knowledge-Integrated Proteomics Web Service with Accurate Statistical Significance Assignment.

Aleksey Y Ogurtsov1, Gelio Alves1, Yi-Kuo Yu1

  • 1National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20894, USA.

Proteomics
|March 26, 2019
PubMed
Summary
This summary is machine-generated.

RAId is a web service that accurately identifies peptides and proteins from mass spectrometry data using rigorous statistics. This tool helps control false identifications, enabling more reliable scientific conclusions in proteomics research.

Keywords:
MS/MS data analysesknowledge-integrated databasepeptide/protein identificationsproportion of false discoveriesstatistical significance assignment

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Area of Science:

  • Proteomics
  • Computational Biology
  • Bioinformatics

Background:

  • Mass spectrometry-based proteomics relies on accurate peptide and protein identification for hypothesis generation and validation.
  • Controlling the number of falsely identified peptides and proteins is crucial for scientifically meaningful conclusions.
  • RAId has been developed over the past decade to address these challenges in peptide and protein identification.

Purpose of the Study:

  • To present the continued development and features of the RAId web service.
  • To highlight RAId's capability in accurate peptide and protein identification from tandem mass spectrometry data.
  • To emphasize RAId's role in controlling false discovery rates for reliable proteomics research.

Main Methods:

  • RAId employs rigorous statistical methods to assign accurate P-values/E-values for peptide and protein identifications.
  • The web service supports various spectra file formats and offers multiple peptide scoring functions and statistical methods.
  • Users can utilize custom or integrated organismal protein databases with annotated information like polymorphisms and post-translational modifications.

Main Results:

  • RAId provides accurate P-values/E-values, enabling confident control of falsely identified peptides and proteins.
  • The web service recognizes diverse spectra file formats, enhancing its versatility.
  • RAId offers a user-friendly interface for displaying, sorting, and downloading identified peptides and proteins.

Conclusions:

  • RAId is a versatile and statistically rigorous web service for accurate peptide and protein identification in mass spectrometry-based proteomics.
  • The tool's ability to control false identifications enhances the reliability of scientific conclusions.
  • RAId is freely available and supports advanced features for database integration and data management.