Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource

View ORCID ProfileKlaas J. van Wijk, View ORCID ProfileTami Leppert, View ORCID ProfileQi Sun, View ORCID ProfileSascha S. Boguraev, View ORCID ProfileZhi Sun, View ORCID ProfileLuis Mendoza, View ORCID ProfileEric W. Deutsch
doi: https://doi.org/10.1101/2021.05.03.442425
Klaas J. van Wijk
aSection of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Klaas J. van Wijk
  • For correspondence: kv35@cornell.edu edeutsch@systemsbiology.org
Tami Leppert
bInstitute for Systems Biology (ISB), Seattle, Washington 98109, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tami Leppert
Qi Sun
cComputational Biology Service Unit, Cornell University, Ithaca, NY 14853
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Qi Sun
Sascha S. Boguraev
aSection of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sascha S. Boguraev
Zhi Sun
bInstitute for Systems Biology (ISB), Seattle, Washington 98109, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zhi Sun
Luis Mendoza
bInstitute for Systems Biology (ISB), Seattle, Washington 98109, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Luis Mendoza
Eric W. Deutsch
bInstitute for Systems Biology (ISB), Seattle, Washington 98109, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Eric W. Deutsch
  • For correspondence: kv35@cornell.edu edeutsch@systemsbiology.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

ABSTRACT

We developed a new resource, the Arabidopsis PeptideAtlas (www.peptideatlas.org/builds/arabidopsis/), to solve central questions about the Arabidopsis proteome, such as the significance of protein splice forms, post-translational modifications (PTMs), or simply obtain reliable information about specific proteins. PeptideAtlas is based on published mass spectrometry (MS) analyses collected through ProteomeXchange and reanalyzed through a uniform processing and metadata annotation pipeline. All matched MS-derived peptide data are linked to spectral, technical and biological metadata. Nearly 40 million out of ∼143 million MSMS spectra were matched to the reference genome Araport11, identifying ∼0.5 million unique peptides and 17858 uniquely identified proteins (only isoform per gene) at the highest confidence level (FDR 0.0004; 2 non-nested peptides ≥ 9 aa each), assigned canonical proteins, and 3543 lower confidence proteins. Physicochemical protein properties were evaluated for targeted identification of unobserved proteins. Additional proteins and isoforms currently not in Araport11 were identified, generated from pseudogenes, alternative start, stops and/or splice variants and sORFs; these features should be considered for updates to the Arabidopsis genome. Phosphorylation can be inspected through a sophisticated PTM viewer. This new PeptideAtlas is integrated with community resources including TAIR, tracks in JBrowse, PPDB and UniProtKB. Subsequent PeptideAtlas builds will incorporate millions more MS data.

One sentence summary A new web resource providing the global community with mass spectrometry-based Arabidopsis proteome information and its spectral, technical and biological metadata integrated with TAIR and JBrowse

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 03, 2021.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource
Klaas J. van Wijk, Tami Leppert, Qi Sun, Sascha S. Boguraev, Zhi Sun, Luis Mendoza, Eric W. Deutsch
bioRxiv 2021.05.03.442425; doi: https://doi.org/10.1101/2021.05.03.442425
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
The Arabidopsis thaliana PeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource
Klaas J. van Wijk, Tami Leppert, Qi Sun, Sascha S. Boguraev, Zhi Sun, Luis Mendoza, Eric W. Deutsch
bioRxiv 2021.05.03.442425; doi: https://doi.org/10.1101/2021.05.03.442425

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Plant Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3504)
  • Biochemistry (7346)
  • Bioengineering (5321)
  • Bioinformatics (20259)
  • Biophysics (10013)
  • Cancer Biology (7742)
  • Cell Biology (11298)
  • Clinical Trials (138)
  • Developmental Biology (6437)
  • Ecology (9950)
  • Epidemiology (2065)
  • Evolutionary Biology (13318)
  • Genetics (9360)
  • Genomics (12581)
  • Immunology (7700)
  • Microbiology (19016)
  • Molecular Biology (7439)
  • Neuroscience (41029)
  • Paleontology (300)
  • Pathology (1229)
  • Pharmacology and Toxicology (2135)
  • Physiology (3157)
  • Plant Biology (6860)
  • Scientific Communication and Education (1272)
  • Synthetic Biology (1895)
  • Systems Biology (5311)
  • Zoology (1089)