A high-quality catalog of the Drosophila melanogaster proteome

Erich Brunner; Christian H Ahrens; Sonali 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 Kregenow; 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, Sonali 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 Kregenow, Albert J R Heck, Ernst Hafen, Ralph SchlapbachRuedi Aebersold

Research output: Contribution to journal › Article › 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
Pages (from-to)	576-83
Number of pages	8
Journal	Nature Biotechnology
Volume	25
Issue number	5
DOIs	https://doi.org/10.1038/nbt1300
Publication status	Published - 2007 May
Externally published	Yes

Free keywords

Amino Acid Sequence
Animals
Databases, Protein
Drosophila Proteins
Drosophila melanogaster
Molecular Sequence Data
Proteome
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

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10.1038/nbt1300

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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., Kregenow, 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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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.",

keywords = "Amino Acid Sequence, Animals, Databases, Protein, Drosophila Proteins, Drosophila melanogaster, Molecular Sequence Data, Proteome, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't",

author = "Erich Brunner and Ahrens, {Christian H} and Sonali 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 Kregenow and Heck, {Albert J R} and Ernst Hafen and Ralph Schlapbach and Ruedi Aebersold",

year = "2007",

month = may,

doi = "10.1038/nbt1300",

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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, Kregenow, 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

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

AU - Brunner, Erich

AU - Ahrens, Christian H

AU - Mohanty, Sonali

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 - Kregenow, Floyd

AU - Heck, Albert J R

AU - Hafen, Ernst

AU - Schlapbach, Ralph

AU - Aebersold, Ruedi

PY - 2007/5

Y1 - 2007/5

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.

KW - Amino Acid Sequence

KW - Animals

KW - Databases, Protein

KW - Drosophila Proteins

KW - Drosophila melanogaster

KW - Molecular Sequence Data

KW - Proteome

KW - Journal Article

KW - Research Support, N.I.H., Extramural

KW - Research Support, Non-U.S. Gov't

U2 - 10.1038/nbt1300

DO - 10.1038/nbt1300

M3 - 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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