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PMID: 18442284 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

A computational strategy to analyze label-free temporal bottom-up proteomics data.

Journal of proteome research ·Vol. 7 ·No. 7 ·2008-07-00 ·Pages 2595-604

Du X, Callister SJ, Manes NP, Adkins JN, Alexandridis RA, Zeng X, Roh JH, Smith WE, Donohue TJ, Kaplan S, Smith RD, Lipton MS

Abstract

Biological systems are in a continual state of flux, which necessitates an understanding of the dynamic nature of protein abundances. The study of protein abundance dynamics has become feasible with recent improvements in mass spectrometry-based quantitative proteomics. However, a number of challenges still remain related to how best to extract biological information from dynamic proteomics data, for example, challenges related to extraneous variability, missing abundance values, and the identification of significant temporal patterns. This paper describes a strategy that addresses these issues and demonstrates its values for analyzing temporal bottom-up proteomics data using data from a Rhodobacter sphaeroides 2.4.1 time-course study.

MeSH Terms
Bacterial Proteins/metabolism Computational Biology Computing Methodologies Proteome/metabolism Proteomics Rhodobacter sphaeroides/metabolism Time Factors
Chemicals
Bacterial Proteins Proteome
Authors & Affiliations
12 authors, click to expand affiliations / ORCID
Du Xiuxia
Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
Callister Stephen J
Manes Nathan P
Adkins Joshua N
Alexandridis Roxana A
Zeng Xiaohua
Roh Jung Hyeob
Smith William E
Donohue Timothy J
Kaplan Samuel
Smith Richard D
Lipton Mary S
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Article Info
Journal
Journal of proteome research
Abbr.
J Proteome Res
ISSN
1535-3893
DOI
10.1021/pr0704837
Published
2008-07-00
Epub
2008-00-29
Pages
2595-604
Language
English
Region
United States
NLM ID
101128775
PMCID
PMC2574618
Subset
IM
Grants
NIGMS NIH HHS · R01 GM075273 · United States
NIGMS NIH HHS · GM075273 · United States
NIGMS NIH HHS · R01 GM075273-02 · United States
NIGMS NIH HHS · R01 GM015590 · United States
NIAID NIH HHS · Y1-AI-4894-01 · United States
NIGMS NIH HHS · GM15590 · United States
External Links
PubMed source DOI: 10.1021/pr0704837 PMC Full Text View journal details
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