Skip to main content
Molecular & Cellular Proteomics

Main menu

  • Home
  • Articles
    • Current Issue
    • Papers in Press
    • Reviews and Minireviews
    • Special Issues
    • Editorials
    • Archive
  • Info for
    • Authors
      • Editorial Policies
      • How to Submit
      • Manuscript Contents & Organization
      • Data Reporting Requirements
      • Publication Charges
    • Reviewers
    • Librarians
    • Advertisers
    • Subscribers
  • Guidelines
    • Proteomic Identification
      • Checklist (PDF)
      • Instructions for Annotated Spectra
      • Tutorial (PDF)
    • Clinical Proteomics
      • Checklist (PDF)
    • Glycomic Identification
      • Checklist (PDF)
    • Targeted Proteomics
      • Checklist (PDF)
    • Data Independent Acquisition
      • Checklist (PDF)
    • Frequently Asked Questions
  • About
    • Mission Statement and Scope
    • Editorial Policies
    • Editorial Board
    • MCP Lectureships
    • Permissions and Licensing
    • Partners
    • Alerts
    • Contact Us

Submit

  • Submit
  • Publications
    • ASBMB
    • Molecular & Cellular Proteomics
    • Journal of Biological Chemistry
    • Journal of Lipid Research

User menu

  • Register
  • Subscribe
  • My alerts
  • Log in
  • My Cart

Search

  • Advanced search
  • Publications
    • ASBMB
    • Molecular & Cellular Proteomics
    • Journal of Biological Chemistry
    • Journal of Lipid Research
  • Register
  • Subscribe
  • My alerts
  • Log in
  • My Cart
Molecular & Cellular Proteomics

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Papers in Press
    • Reviews and Minireviews
    • Special Issues
    • Editorials
    • Archive
  • Info for
    • Authors
      • Editorial Policies
      • How to Submit
      • Manuscript Contents & Organization
      • Data Reporting Requirements
      • Publication Charges
    • Reviewers
    • Librarians
    • Advertisers
    • Subscribers
  • Guidelines
    • Proteomic Identification
      • Checklist (PDF)
      • Instructions for Annotated Spectra
      • Tutorial (PDF)
    • Clinical Proteomics
      • Checklist (PDF)
    • Glycomic Identification
      • Checklist (PDF)
    • Targeted Proteomics
      • Checklist (PDF)
    • Data Independent Acquisition
      • Checklist (PDF)
    • Frequently Asked Questions
  • About
    • Mission Statement and Scope
    • Editorial Policies
    • Editorial Board
    • MCP Lectureships
    • Permissions and Licensing
    • Partners
    • Alerts
    • Contact Us
  • Submit
Technological Innovation and Resources

Quantifying homologous proteins and proteoforms

Dmitry Malioutov, Tianchi Chen, Edoardo Airoldi, View ORCID ProfileJacob D. Jaffe, View ORCID ProfileBogdan Budnik and View ORCID ProfileNikolai Slavov  Correspondence email
Molecular & Cellular Proteomics October 3, 2018, mcp.TIR118.000947; https://doi.org/10.1074/mcp.TIR118.000947
Dmitry Malioutov
IBM, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tianchi Chen
Northeastern University, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Edoardo Airoldi
Broad Institute, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jacob D. Jaffe
Proteomics, Massachusetts Institute of Technology, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jacob D. Jaffe
Bogdan Budnik
Harvard University
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bogdan Budnik
Nikolai Slavov
Northeastern University, United States of America
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nikolai Slavov
  • For correspondence: nslavov@alum.mit.edu
  • Article
  • Figures & Data
  • Info & Metrics
  • eLetters
  • PDF
Loading

Abstract

Many proteoforms – arising from alternative splicing, post-translational modifications (PTM), or paralogous genes – have distinct biological functions, such as histone PTM proteoforms. However, their quantification by existing bottom-up mass–spectrometry (MS) methods is undermined by peptide-specific biases. To avoid these biases, we developed and implemented a first-principles model (HIquant ) for quantifying proteoform stoichiometries. We characterized when MS data allow inferring proteoform stoichiometries by HIquant and derived an algorithm for optimal inference. We applied this algorithm to infer proteoform stoichiometries in two experimental systems that supported rigorous bench-marking: alkylated proteoforms spiked-in at known ratios and endogenous histone 3 PTM proteoforms quantified relative to internal heavy standards. When compared to the benchmarks, the proteoform stoichiometries interfered by HIquant without using external standards had relative error of 5 − 15% for simple proteoforms and 20 − 30% for complex proteoforms. A HIquant server is implemented at: https://web.northeastern.edu/slavov/2014_HIquant/

  • Algorithms
  • Bioinformatics
  • Bioinformatics software
  • Mass Spectrometry
  • Mathematical Modeling

Footnotes

  • Author contributions: D.M., T.C., B.B., and N.S. performed research; D.M., E.A., J.D.J., and N.S. contributed new reagents/analytic tools; D.M. and N.S. analyzed data; J.D.J. and N.S. wrote the paper; N.S. designed research.

  • Received June 28, 2018.
  • Accepted October 3, 2018.
  • Published under license by The American Society for Biochemistry and Molecular Biology, Inc.
PreviousNext
Back to top
Download PDF
Article Alerts
Sign In to Email Alerts with your Email Address
Email Article

Thank you for your interest in spreading the word on Molecular & Cellular Proteomics.

NOTE: We only request your email address so that the person you are recommending the page to knows that you wanted them to see it, and that it is not junk mail. We do not capture any email address.

Enter multiple addresses on separate lines or separate them with commas.
Quantifying homologous proteins and proteoforms
(Your Name) has sent you a message from Molecular & Cellular Proteomics
(Your Name) thought you would like to see the Molecular & Cellular Proteomics web site.
Citation Tools
Quantifying homologous proteins and proteoforms
Dmitry Malioutov, Tianchi Chen, Edoardo Airoldi, Jacob D. Jaffe, Bogdan Budnik, Nikolai Slavov
Molecular & Cellular Proteomics October 3, 2018, mcp.TIR118.000947; DOI: 10.1074/mcp.TIR118.000947

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero

Request Permissions

Share
Quantifying homologous proteins and proteoforms
Dmitry Malioutov, Tianchi Chen, Edoardo Airoldi, Jacob D. Jaffe, Bogdan Budnik, Nikolai Slavov
Molecular & Cellular Proteomics October 3, 2018, mcp.TIR118.000947; DOI: 10.1074/mcp.TIR118.000947
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Jump to section

  • Article
  • Figures & Data
  • eLetters
  • Info & Metrics
  • PDF

  • Follow MCP on Twitter
  • RSS feeds
  • Email

Articles

  • Current Issue
  • Papers in Press
  • Archive

For Authors

  • Submit a Manuscript
  • Info for Authors

Guidelines

  • Proteomic Identification
  • Clinical Proteomics
  • Glycomic Identification
  • Targeted Proteomics
  • Frequently Asked Questions

About MCP

  • About the Journal
  • Permissions and Licensing
  • Advertisers
  • Subscribers

ASBMB Publications

  • Molecular & Cellular Proteomics
  • Journal of Biological Chemistry
  • Journal of Lipid Research
  • ASBMB Today

© 2019 American Society for Biochemistry and Molecular Biology | Privacy Policy

MCP Print ISSN 1535-9476 Online ISSN 1535-9484

Powered by HighWire