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Bioinformatic challenges in targeted proteomics.

Publication ,  Journal Article
Reker, D; Malmström, L
Published in: Journal of proteome research
September 2012

Selected reaction monitoring mass spectrometry is an emerging targeted proteomics technology that allows for the investigation of complex protein samples with high sensitivity and efficiency. It requires extensive knowledge about the sample for the many parameters needed to carry out the experiment to be set appropriately. Most studies today rely on parameter estimation from prior studies, public databases, or from measuring synthetic peptides. This is efficient and sound, but in absence of prior data, de novo parameter estimation is necessary. Computational methods can be used to create an automated framework to address this problem. However, the number of available applications is still small. This review aims at giving an orientation on the various bioinformatical challenges. To this end, we state the problems in classical machine learning and data mining terms, give examples of implemented solutions and provide some room for alternatives. This will hopefully lead to an increased momentum for the development of algorithms and serve the needs of the community for computational methods. We note that the combination of such methods in an assisted workflow will ease both the usage of targeted proteomics in experimental studies as well as the further development of computational approaches.

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Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

September 2012

Volume

11

Issue

9

Start / End Page

4393 / 4402

Related Subject Headings

  • Proteomics
  • Proteins
  • Mass Spectrometry
  • Databases, Protein
  • Data Mining
  • Computational Biology
  • Biochemistry & Molecular Biology
  • Artificial Intelligence
  • Algorithms
  • 34 Chemical sciences
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Reker, D., & Malmström, L. (2012). Bioinformatic challenges in targeted proteomics. Journal of Proteome Research, 11(9), 4393–4402. https://doi.org/10.1021/pr300276f
Reker, Daniel, and Lars Malmström. “Bioinformatic challenges in targeted proteomics.Journal of Proteome Research 11, no. 9 (September 2012): 4393–4402. https://doi.org/10.1021/pr300276f.
Reker D, Malmström L. Bioinformatic challenges in targeted proteomics. Journal of proteome research. 2012 Sep;11(9):4393–402.
Reker, Daniel, and Lars Malmström. “Bioinformatic challenges in targeted proteomics.Journal of Proteome Research, vol. 11, no. 9, Sept. 2012, pp. 4393–402. Epmc, doi:10.1021/pr300276f.
Reker D, Malmström L. Bioinformatic challenges in targeted proteomics. Journal of proteome research. 2012 Sep;11(9):4393–4402.
Journal cover image

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

September 2012

Volume

11

Issue

9

Start / End Page

4393 / 4402

Related Subject Headings

  • Proteomics
  • Proteins
  • Mass Spectrometry
  • Databases, Protein
  • Data Mining
  • Computational Biology
  • Biochemistry & Molecular Biology
  • Artificial Intelligence
  • Algorithms
  • 34 Chemical sciences