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Data Independent Acquisition analysis in ProHits 4.0.

Guomin Liu1, James D R Knight1, Jian Ping Zhang1

  • 1Centre for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.

Journal of Proteomics
|May 3, 2016
PubMed
Summary

ProHits 4.0 enhances affinity proteomics by integrating Data-Independent Acquisition tools for robust interaction analysis. This updated LIMS streamlines data management, quantification, and deposition for interaction proteomics studies.

Keywords:
Affinity purification coupled to mass spectrometryData Independent AcquisitionLaboratory Information Management SystemMass spectrometryProtein-protein interactionsProteomics

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Area of Science:

  • Proteomics
  • Biochemistry
  • Bioinformatics

Background:

  • Affinity purification coupled with mass spectrometry (AP-MS) is vital for identifying protein interactions.
  • Existing workflows require careful design and analysis for accurate results.
  • ProHits, a Laboratory Information Management System (LIMS), was previously developed to manage AP-MS data.

Purpose of the Study:

  • To update ProHits to support Data-Independent Acquisition (DIA) workflows.
  • To enhance ProHits with new identification, quantification, and scoring tools.
  • To improve data management and deposition for interaction proteomics.

Main Methods:

  • Integration of DIA identification software (DIA-Umpire, MSPLIT-DIA).
  • Inclusion of quantification tools (DIA-Umpire, targeted extraction) and enrichment assessment (mapDIA).
  • Implementation of SAINT-intensity for scoring interactions and iProphet pipeline support.

Main Results:

  • ProHits 4.0 now supports DIA-based proteomics experiments.
  • Enhanced tools for identification, quantification, and scoring of protein interactions.
  • Improved data deposition into ProteomeXchange and enhanced visualization.

Conclusions:

  • ProHits 4.0 provides a comprehensive suite for affinity proteomics, particularly for DIA studies.
  • The updated system facilitates transparent and efficient analysis of complex proteomics data.
  • ProHits 4.0 streamlines data management from sample tracking to public repository deposition.