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Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

Thilo Muth, Dirk Benndorf, Udo Reichl, Erdmann Rapp and Lennart Martens UGent (2013) MOLECULAR BIOSYSTEMS. 9(4). p.578-585
abstract
In the past years the integral study of microbial communities of varying complexity has gained increasing research interest. Mass spectrometry-driven metaproteomics enables the analysis of such communities on the functional level, but this fledgling field still faces various technical and semantic challenges regarding experimental data analysis and interpretation. In the present review, we outline the hurdles involved and attempt to cover the most valuable methods and software implementations available to researchers in the field today. Beyond merely focusing on protein identification, we provide an overview on different data pre- and post-processing steps, such as metabolic pathway analysis, that can be useful in a typical metaproteomics workflow. Finally, we briefly discuss directions for future work.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (review)
publication status
published
subject
keyword
TOOL, PEPTIDE IDENTIFICATION, GENE PREDICTION, TANDEM MASS-SPECTRA, SPECTROMETRY DATA, PROTEIN IDENTIFICATION, SACCHAROMYCES-CEREVISIAE, SHOTGUN PROTEOMIC DATA, MICROBIAL COMMUNITIES, METABOLIC PATHWAYS
journal title
MOLECULAR BIOSYSTEMS
Mol. Biosyst.
volume
9
issue
4
pages
578 - 585
Web of Science type
Review
Web of Science id
000315908800006
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
3.183 (2013)
JCR rank
119/291 (2013)
JCR quartile
2 (2013)
ISSN
1742-206X
DOI
10.1039/c2mb25415h
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
3193145
handle
http://hdl.handle.net/1854/LU-3193145
date created
2013-04-15 09:56:18
date last changed
2016-12-19 15:45:59
@article{3193145,
  abstract     = {In the past years the integral study of microbial communities of varying complexity has gained increasing research interest. Mass spectrometry-driven metaproteomics enables the analysis of such communities on the functional level, but this fledgling field still faces various technical and semantic challenges regarding experimental data analysis and interpretation. In the present review, we outline the hurdles involved and attempt to cover the most valuable methods and software implementations available to researchers in the field today. Beyond merely focusing on protein identification, we provide an overview on different data pre- and post-processing steps, such as metabolic pathway analysis, that can be useful in a typical metaproteomics workflow. Finally, we briefly discuss directions for future work.},
  author       = {Muth, Thilo and Benndorf, Dirk and Reichl, Udo and Rapp, Erdmann and Martens, Lennart},
  issn         = {1742-206X},
  journal      = {MOLECULAR BIOSYSTEMS},
  keyword      = {TOOL,PEPTIDE IDENTIFICATION,GENE PREDICTION,TANDEM MASS-SPECTRA,SPECTROMETRY DATA,PROTEIN IDENTIFICATION,SACCHAROMYCES-CEREVISIAE,SHOTGUN PROTEOMIC DATA,MICROBIAL COMMUNITIES,METABOLIC PATHWAYS},
  language     = {eng},
  number       = {4},
  pages        = {578--585},
  title        = {Searching for a needle in a stack of needles: challenges in metaproteomics data analysis},
  url          = {http://dx.doi.org/10.1039/c2mb25415h},
  volume       = {9},
  year         = {2013},
}

Chicago
Muth, Thilo, Dirk Benndorf, Udo Reichl, Erdmann Rapp, and Lennart Martens. 2013. “Searching for a Needle in a Stack of Needles: Challenges in Metaproteomics Data Analysis.” Molecular Biosystems 9 (4): 578–585.
APA
Muth, T., Benndorf, D., Reichl, U., Rapp, E., & Martens, L. (2013). Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. MOLECULAR BIOSYSTEMS, 9(4), 578–585.
Vancouver
1.
Muth T, Benndorf D, Reichl U, Rapp E, Martens L. Searching for a needle in a stack of needles: challenges in metaproteomics data analysis. MOLECULAR BIOSYSTEMS. 2013;9(4):578–85.
MLA
Muth, Thilo, Dirk Benndorf, Udo Reichl, et al. “Searching for a Needle in a Stack of Needles: Challenges in Metaproteomics Data Analysis.” MOLECULAR BIOSYSTEMS 9.4 (2013): 578–585. Print.