A high-quality catalog of the Drosophila melanogaster proteome

Erich Brunner; Christian H. Ahrens; Sonaly Mohanty; Hansruedi Baetschmann; Sandra Loevenich; Frank Potthast; Eric W. Deutsch; Christian Panse; Ulrik de Lichtenberg; Oliver Rinner; Hookeun Lee; Patrick G. A. Pedrioli; Johan Malmstrom; Katja Koehler; Sabine Schrimpf; Jeroen Krijgsveld; Floyd Kregenov; Albert J. R. Heck; Ernst Hafen; Ralph Schlapbach; Ruedi Aebersold

doi:10.1038/nbt1300

A high-quality catalog of the Drosophila melanogaster proteome

Erich Brunner, Christian H. Ahrens, Sonaly Mohanty, Hansruedi Baetschmann, Sandra Loevenich, Frank Potthast, Eric W. Deutsch, Christian Panse, Ulrik de Lichtenberg, Oliver Rinner, Hookeun Lee, Patrick G. A. Pedrioli, Johan Malmstrom, Katja Koehler, Sabine Schrimpf, Jeroen Krijgsveld, Floyd Kregenov, Albert J. R. Heck, Ernst Hafen, Ralph SchlapbachRuedi Aebersold

Research output: Contribution to journal › Journal article › Research › peer-review

Abstract

Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.

Original language	English
Journal	Nature Biotechnology
Volume	25
Issue number	5
Pages (from-to)	576-83
ISSN	1087-0156
DOIs	https://doi.org/10.1038/nbt1300
Publication status	Published - 2007

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Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E. W., Panse, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P. G. A., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgsveld, J., Kregenov, F., Heck, A. J. R., Hafen, E., ... Aebersold, R. (2007). A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology, 25(5), 576-83. https://doi.org/10.1038/nbt1300

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title = "A high-quality catalog of the Drosophila melanogaster proteome",

abstract = "Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.",

author = "Erich Brunner and Ahrens, {Christian H.} and Sonaly Mohanty and Hansruedi Baetschmann and Sandra Loevenich and Frank Potthast and Deutsch, {Eric W.} and Christian Panse and {de Lichtenberg}, Ulrik and Oliver Rinner and Hookeun Lee and Pedrioli, {Patrick G. A.} and Johan Malmstrom and Katja Koehler and Sabine Schrimpf and Jeroen Krijgsveld and Floyd Kregenov and Heck, {Albert J. R.} and Ernst Hafen and Ralph Schlapbach and Ruedi Aebersold",

year = "2007",

doi = "10.1038/nbt1300",

language = "English",

volume = "25",

pages = "576--83",

journal = "Nature Biotechnology",

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Brunner, E, Ahrens, CH, Mohanty, S, Baetschmann, H, Loevenich, S, Potthast, F, Deutsch, EW, Panse, C, de Lichtenberg, U, Rinner, O, Lee, H, Pedrioli, PGA, Malmstrom, J, Koehler, K, Schrimpf, S, Krijgsveld, J, Kregenov, F, Heck, AJR, Hafen, E, Schlapbach, R & Aebersold, R 2007, 'A high-quality catalog of the Drosophila melanogaster proteome', Nature Biotechnology, vol. 25, no. 5, pp. 576-83. https://doi.org/10.1038/nbt1300

TY - JOUR

T1 - A high-quality catalog of the Drosophila melanogaster proteome

AU - Brunner, Erich

AU - Ahrens, Christian H.

AU - Mohanty, Sonaly

AU - Baetschmann, Hansruedi

AU - Loevenich, Sandra

AU - Potthast, Frank

AU - Deutsch, Eric W.

AU - Panse, Christian

AU - de Lichtenberg, Ulrik

AU - Rinner, Oliver

AU - Lee, Hookeun

AU - Pedrioli, Patrick G. A.

AU - Malmstrom, Johan

AU - Koehler, Katja

AU - Schrimpf, Sabine

AU - Krijgsveld, Jeroen

AU - Kregenov, Floyd

AU - Heck, Albert J. R.

AU - Hafen, Ernst

AU - Schlapbach, Ralph

AU - Aebersold, Ruedi

PY - 2007

Y1 - 2007

N2 - Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.

AB - Understanding how proteins and their complex interaction networks convert the genomic information into a dynamic living organism is a fundamental challenge in biological sciences. As an important step towards understanding the systems biology of a complex eukaryote, we cataloged 63% of the predicted Drosophila melanogaster proteome by detecting 9,124 proteins from 498,000 redundant and 72,281 distinct peptide identifications. This unprecedented high proteome coverage for a complex eukaryote was achieved by combining sample diversity, multidimensional biochemical fractionation and analysis-driven experimentation feedback loops, whereby data collection is guided by statistical analysis of prior data. We show that high-quality proteomics data provide crucial information to amend genome annotation and to confirm many predicted gene models. We also present experimentally identified proteotypic peptides matching approximately 50% of D. melanogaster gene models. This library of proteotypic peptides should enable fast, targeted and quantitative proteomic studies to elucidate the systems biology of this model organism.

U2 - 10.1038/nbt1300

DO - 10.1038/nbt1300

M3 - Journal article

C2 - 17450130

SN - 1087-0156

VL - 25

SP - 576

EP - 583

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 5

ER -

A high-quality catalog of the Drosophila melanogaster proteome

Abstract

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