NDLI: Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Krug, Karsten Carpy, Alejandro Behrends, Gesa Matic, Katarina Soares, Nelson C. Macek, Boris
Description	Country affiliation: Germany Author Affiliation: Krug K ( Proteome Center Tuebingen, University of Tuebingen, 72076 Tuebingen, Germany.)
Abstract	Recent advances in mass spectrometry (MS) have led to increased applications of shotgun proteomics to the refinement of genome annotation. The typical 'proteo-genomic' workflows rely on the mapping of peptide MS/MS spectra onto databases derived via six-frame translation of the genome sequence. These databases contain a large proportion of spurious protein sequences which make the statistical confidence of the resulting peptide spectrum matches difficult to assess. Here we performed a comprehensive analysis of the Escherichia coli proteome using LTQ-Orbitrap MS and mapped the corresponding MS/MS spectra onto a six-frame translation of the E. coli genome. We hypothesized that the protein-coding part of the E. coli genome approaches complete annotation and that the majority of six frame-specific (novel) peptide spectrum matches can be considered as false positive identifications. We confirm our hypothesis by showing that the posterior error probability distribution of novel hits is almost identical to that of reversed (decoy) hits; this enables us to estimate the sensitivity, specificity, accuracy, and false discovery rate in a typical bacterial proteo-genomic dataset. We use two complementary computational frameworks for processing and statistical assessment of MS/MS data: MaxQuant and Trans-Proteomic Pipeline. We show that MaxQuant achieves a more sensitive six-frame database search with an acceptable false discovery rate and is therefore well suited for global genome reannotation applications, whereas the Trans-Proteomic Pipeline achieves higher specificity and is well suited for high-confidence validation. The use of a small and well-annotated bacterial genome enables us to address genome coverage achieved in state-of-the-art bacterial proteomics: identified peptide sequences mapped to all expressed E. coli proteins but covered 31.7% of the protein-coding genome sequence. Our results show that false discovery rates can be substantially underestimated even in 'simple' proteo-genomic experiments obtained by means of high-accuracy MS and point to the necessity of further improvements concerning the coverage of peptide sequences by MS-based methods.
File Format	HTM / HTML
ISSN	15359476
e-ISSN	15359484
DOI	10.1074/mcp.M113.029165
Journal	Molecular & Cellular Proteomics
Issue Number	11
Volume Number	12
Language	English
Publisher	American Society for Biochemistry and Molecular Biology
Publisher Date	2013-11-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Proteomics Escherichia Coli Proteins Genetics Metabolism Genomics Proteomics Databases, Genetic Databases, Protein Escherichia Coli K12 Genome, Bacterial Statistics & Numerical Data Proteome Tandem Mass Spectrometry Research Support, Non-u.s. Gov't
Content Type	Text
Resource Type	Article
Subject	Medicine Analytical Chemistry Molecular Biology Biochemistry

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments*

The Escherichia coli peripheral inner membrane proteome.

Identification of bacterial factors involved in type 1 fimbria expression using an Escherichia coli K12 proteome chip.

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

Identification and relative quantification of proteins in Escherichia coli proteome by 'up-front' collision-induced dissociation.

Large-scale identification of protein-protein interaction of Escherichia coli K-12.

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome.

Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.

Similar Documents

Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments*

The Escherichia coli peripheral inner membrane proteome.

Identification of bacterial factors involved in type 1 fimbria expression using an Escherichia coli K12 proteome chip.

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

Identification and relative quantification of proteins in Escherichia coli proteome by 'up-front' collision-induced dissociation.

Large-scale identification of protein-protein interaction of Escherichia coli K-12.

Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline.

Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.

Reaching for the deep proteome: recent nano liquid chromatography coupled with tandem mass spectrometry-based studies on the deep proteome.

Deep coverage of the Escherichia coli proteome enables the assessment of false discovery rates in simple proteogenomic experiments.