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Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.

Publication ,  Journal Article
Van, PT; Schmid, AK; King, NL; Kaur, A; Pan, M; Whitehead, K; Koide, T; Facciotti, MT; Goo, YA; Deutsch, EW; Reiss, DJ; Mallick, P; Baliga, NS
Published in: Journal of proteome research
September 2008

The relatively small numbers of proteins and fewer possible post-translational modifications in microbes provide a unique opportunity to comprehensively characterize their dynamic proteomes. We have constructed a PeptideAtlas (PA) covering 62.7% of the predicted proteome of the extremely halophilic archaeon Halobacterium salinarum NRC-1 by compiling approximately 636 000 tandem mass spectra from 497 mass spectrometry runs in 88 experiments. Analysis of the PA with respect to biophysical properties of constituent peptides, functional properties of parent proteins of detected peptides, and performance of different mass spectrometry approaches has highlighted plausible strategies for improving proteome coverage and selecting signature peptides for targeted proteomics. Notably, discovery of a significant correlation between absolute abundances of mRNAs and proteins has helped identify low abundance of proteins as the major limitation in peptide detection. Furthermore, we have discovered that iTRAQ labeling for quantitative proteomic analysis introduces a significant bias in peptide detection by mass spectrometry. Therefore, despite identifying at least one proteotypic peptide for almost all proteins in the PA, a context-dependent selection of proteotypic peptides appears to be the most effective approach for targeted proteomics.

Duke Scholars

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

September 2008

Volume

7

Issue

9

Start / End Page

3755 / 3764

Related Subject Headings

  • Solubility
  • Proteome
  • Molecular Sequence Data
  • Mass Spectrometry
  • Isoelectric Point
  • Halobacterium salinarum
  • Biochemistry & Molecular Biology
  • Archaeal Proteins
  • Amino Acid Sequence
  • 34 Chemical sciences
 

Citation

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Van, P. T., Schmid, A. K., King, N. L., Kaur, A., Pan, M., Whitehead, K., … Baliga, N. S. (2008). Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of Proteome Research, 7(9), 3755–3764. https://doi.org/10.1021/pr800031f
Van, Phu T., Amy K. Schmid, Nichole L. King, Amardeep Kaur, Min Pan, Kenia Whitehead, Tie Koide, et al. “Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.Journal of Proteome Research 7, no. 9 (September 2008): 3755–64. https://doi.org/10.1021/pr800031f.
Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, et al. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of proteome research. 2008 Sep;7(9):3755–64.
Van, Phu T., et al. “Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage.Journal of Proteome Research, vol. 7, no. 9, Sept. 2008, pp. 3755–64. Epmc, doi:10.1021/pr800031f.
Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS. Halobacterium salinarum NRC-1 PeptideAtlas: toward strategies for targeted proteomics and improved proteome coverage. Journal of proteome research. 2008 Sep;7(9):3755–3764.
Journal cover image

Published In

Journal of proteome research

DOI

EISSN

1535-3907

ISSN

1535-3893

Publication Date

September 2008

Volume

7

Issue

9

Start / End Page

3755 / 3764

Related Subject Headings

  • Solubility
  • Proteome
  • Molecular Sequence Data
  • Mass Spectrometry
  • Isoelectric Point
  • Halobacterium salinarum
  • Biochemistry & Molecular Biology
  • Archaeal Proteins
  • Amino Acid Sequence
  • 34 Chemical sciences