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Cited by 13Mass Spectrometry Techniques and ApplicationsProtein Structure and DynamicsEnzyme Structure and Function

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Predicting ion mobility collision cross sections using projection approximation with ROSIE-PARCS webserver

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Turzo, S M Bargeen Alam, Seffernick, Justin T, Lyskov, Sergey, Lindert, Steffen·2023·Briefings in Bioinformatics
DOI 10.1093/bib/bbad308PMC PMC10516336

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Abstract

Ion mobility coupled to mass spectrometry informs on the shape and size of protein structures in the form of a collision cross section (CCSIM). Although there are several computational methods for predicting CCSIM based on protein structures, including our previously developed projection approximation using rough circular shapes (PARCS), the process usually requires prior experience with the command-line interface. To overcome this challenge, here we present a web application on the Rosetta Online Server that Includes Everyone (ROSIE) webserver to predict CCSIM from protein structure using projection approximation with PARCS. In this web interface, the user is only required to provide one or more PDB files as input. Results from our case studies suggest that CCSIM predictions (with ROSIE-PARCS) are highly accurate with an average error of 6.12%. Furthermore, the absolute difference between CCSIM and CCSPARCS can help in distinguishing accurate from inaccurate AlphaFold2 protein structure predictions. ROSIE-PARCS is designed with a user-friendly interface, is available publicly and is free to use. The ROSIE-PARCS web interface is supported by all major web browsers and can be accessed via this link (https://rosie.graylab.jhu.edu).

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Metadata

Authors
Turzo, S. M. B. A., Seffernick, J. T., Lyskov, S., & Lindert, S.
Affiliations
  • Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University , Columbus, OH 43210 , USA
  • The Ohio State University (US)
  • Johns Hopkins University (US)
Corresponding author
Lindert, Steffen
ORCID
Venue
Briefings in Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2023-08-22
Volume
24
Issue
5
ISSN
  • 1467-5463 (ISSN-L)
  • 1477-4054
DOI
10.1093/bib/bbad308
PMC
PMC10516336
OpenAlex
W4386084210
Cited by
13
References
3
Citations by year
2026: 5 · 2025: 4 · 2024: 2 · 2023: 2
FWCI
1.20
Type
journal article
Language
en
Open access
Licence
academic.oup.com/pages/standard-publication-reuse-rights (vor)
Locations
  • Briefings in Bioinformatics (publishedVersion)
  • ChemRxiv (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Institutes of Health (P41 GM128577)
  • Sloan Research Fellowship
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
projection approximation, PARCS, web server, protein structure, ion mobility mass spectrometry
MeSH terms
Ion Mobility Spectrometry, Algorithms, Artificial Intelligence, Buffers, Gases, Proteins, Software, User-Computer Interface, Internet, Datasets as Topic, Open Access Publishing

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