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PMID: 19788317 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Integrated algorithms for high-throughput examination of covalently labeled biomolecules by structural mass spectrometry.

Analytical chemistry ·Vol. 81 ·No. 19 ·2009-10-01 ·Pages 8141-9

Kaur P, Kiselar JG, Chance MR

Abstract

Mass spectrometry based structural proteomics approaches for probing protein structures are increasingly gaining in popularity. The potential for such studies is limited because of the lack of analytical techniques for the automated interpretation of resulting data. In this article, a suite of algorithms called ProtMapMS is developed, integrated, and implemented specifically for the comprehensive automatic analysis of mass spectrometry data obtained for protein structure studies using covalent labeling. The functions include data format conversion, mass spectrum interpretation, detection, and verification of all peptide species, confirmation of the modified peptide products, and quantification of the extent of peptide modification. The results thus obtained provide valuable data for use in combination with computational approaches for protein structure modeling. The structures of both monomeric and hexameric forms of insulin were investigated by oxidative protein footprinting followed by high-resolution mass spectrometry. The resultant data was analyzed both manually and using ProtMapMS without any manual intervention. The results obtained using the two methods were found to be in close agreement and overall were consistent with predictions from the crystallographic structure.

MeSH Terms
Algorithms Amino Acid Sequence Humans Hydroxyl Radical/chemistry Insulin/chemistry Mass Spectrometry/methods Oxidation-Reduction Proteomics
Chemicals
Insulin Hydroxyl Radical
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Kaur Parminder
Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, USA. pkhatra@case.edu
Kiselar Janna G
Chance Mark R
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Article Info
Journal
Analytical chemistry
Abbr.
Anal Chem
ISSN
1520-6882
DOI
10.1021/ac9013644
Email
pkhatra@case.edu
Published
2009-10-01
Pages
8141-9
Language
English
Region
United States
NLM ID
0370536
PMCID
PMC2764328
Subset
IM
Grants
NIBIB NIH HHS · P41 EB001979-26 · United States
NIGMS NIH HHS · U54-GM-074945 · United States
NIGMS NIH HHS · U54 GM074945 · United States
NIBIB NIH HHS · P30 EB009998 · United States
NIBIB NIH HHS · P30 EB009998-01 · United States
NIBIB NIH HHS · P41-EB-01979 · United States
NIBIB NIH HHS · P41 EB001979-26S1 · United States
NIBIB NIH HHS · P41 EB001979 · United States
External Links
PubMed source DOI: 10.1021/ac9013644 PMC Full Text View journal details
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