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

(2013) MOLECULAR BIOSYSTEMS. 9(4). p.578-585
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Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
TOOL, PEPTIDE IDENTIFICATION, GENE PREDICTION, TANDEM MASS-SPECTRA, SPECTROMETRY DATA, PROTEIN IDENTIFICATION, SACCHAROMYCES-CEREVISIAE, SHOTGUN PROTEOMIC DATA, MICROBIAL COMMUNITIES, METABOLIC PATHWAYS

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Citation

Please use this url to cite or link to this publication:

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.
@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},
}

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