Advertisement
MCP
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
QUICK SEARCH:   [advanced]


     

Originally published In Press as doi:10.1074/mcp.R500012-MCP200 on July 11, 2005.
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
R500012-MCP200v1
4/10/1419    most recent
Right arrow Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when eLetters are posted
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Glossary
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Nesvizhskii, A. I.
Right arrow Articles by Aebersold, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Nesvizhskii, A. I.
Right arrow Articles by Aebersold, R.
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Molecular & Cellular Proteomics 4:1419-1440, 2005.
© 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Tutorial

Interpretation of Shotgun Proteomic Data

The Protein Inference Problem*

Alexey I. Nesvizhskii{ddagger},§ and Ruedi Aebersold{ddagger},¶

From the {ddagger} Institute for Systems Biology, Seattle, Washington 98103 and Institute for Molecular Systems Biology, ETH-Zurich, CH-8093 Zurich, Switzerland

The shotgun proteomic strategy based on digesting proteins into peptides and sequencing them using tandem mass spectrometry and automated database searching has become the method of choice for identifying proteins in most large scale studies. However, the peptide-centric nature of shotgun proteomics complicates the analysis and biological interpretation of the data especially in the case of higher eukaryote organisms. The same peptide sequence can be present in multiple different proteins or protein isoforms. Such shared peptides therefore can lead to ambiguities in determining the identities of sample proteins. In this article we illustrate the difficulties of interpreting shotgun proteomic data and discuss the need for common nomenclature and transparent informatic approaches. We also discuss related issues such as the state of protein sequence databases and their role in shotgun proteomic analysis, interpretation of relative peptide quantification data in the presence of multiple protein isoforms, the integration of proteomic and transcriptional data, and the development of a computational infrastructure for the integration of multiple diverse datasets.

§ To whom correspondence should be addressed: Inst. for Systems Biology, 1441 N. 34th St., Seattle, WA 98103. Tel.: 206-732-1245; Fax: 206-732-1299; E-mail: nesvi{at}systemsbiology.org


Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 Mol. Cell. ProteomicsHome page
L. Reiter, M. Claassen, S. P. Schrimpf, M. Jovanovic, A. Schmidt, J. M. Buhmann, M. O. Hengartner, and R. Aebersold
Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry
Mol. Cell. Proteomics, November 1, 2009; 8(11): 2405 - 2417.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. A. Grobei, E. Qeli, E. Brunner, H. Rehrauer, R. Zhang, B. Roschitzki, K. Basler, C. H. Ahrens, and U. Grossniklaus
Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function
Genome Res., October 1, 2009; 19(10): 1786 - 1800.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
L. L. Elo, J. Hiissa, J. Tuimala, A. Kallio, E. Korpelainen, and T. Aittokallio
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets
Brief Bioinform, September 1, 2009; 10(5): 547 - 555.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. Gnad, M. Oroshi, E. Birney, and M. Mann
MAPU 2.0: high-accuracy proteomes mapped to genomes
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D902 - D906.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
H. Choi, D. Fermin, and A. I. Nesvizhskii
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics
Mol. Cell. Proteomics, December 1, 2008; 7(12): 2373 - 2385.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
K. Helsens, E. Timmerman, J. Vandekerckhove, K. Gevaert, and L. Martens
Peptizer, a Tool for Assessing False Positive Peptide Identifications and Manually Validating Selected Results
Mol. Cell. Proteomics, December 1, 2008; 7(12): 2364 - 2372.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
X. Chen, P. J. Ulintz, E. S. Simon, J. A. Williams, and P. C. Andrews
Global Topology Analysis of Pancreatic Zymogen Granule Membrane Proteins
Mol. Cell. Proteomics, December 1, 2008; 7(12): 2323 - 2336.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
A. Ramos-Fernandez, A. Paradela, R. Navajas, and J. P. Albar
Generalized Method for Probability-based Peptide and Protein Identification from Tandem Mass Spectrometry Data and Sequence Database Searching
Mol. Cell. Proteomics, September 1, 2008; 7(9): 1748 - 1754.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
P. J. Ulintz, B. Bodenmiller, P. C. Andrews, R. Aebersold, and A. I. Nesvizhskii
Investigating MS2/MS3 Matching Statistics: A Model For Coupling Consecutive Stage Mass Spectrometry Data For Increased Peptide Identification Confidence
Mol. Cell. Proteomics, January 1, 2008; 7(1): 71 - 87.
[Abstract] [Full Text] [PDF]

Home page
 J. Virol.Home page
J. Wu, Q. Lin, T. K. Lim, T. Liu, and C.-L. Hew
White Spot Syndrome Virus Proteins and Differentially Expressed Host Proteins Identified in Shrimp Epithelium by Shotgun Proteomics and Cleavable Isotope-Coded Affinity Tag
J. Virol., November 1, 2007; 81(21): 11681 - 11689.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
A. K. Schmid, D. J. Reiss, A. Kaur, M. Pan, N. King, P. T. Van, L. Hohmann, D. B. Martin, and N. S. Baliga
The anatomy of microbial cell state transitions in response to oxygen
Genome Res., October 1, 2007; 17(10): 1399 - 1413.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
I. V. Shilov, S. L. Seymour, A. A. Patel, A. Loboda, W. H. Tang, S. P. Keating, C. L. Hunter, L. M. Nuwaysir, and D. A. Schaeffer
The Paragon Algorithm, a Next Generation Search Engine That Uses Sequence Temperature Values and Feature Probabilities to Identify Peptides from Tandem Mass Spectra
Mol. Cell. Proteomics, September 1, 2007; 6(9): 1638 - 1655.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Feng, D. Q. Naiman, and B. Cooper
Probability-based pattern recognition and statistical framework for randomization: modeling tandem mass spectrum/peptide sequence false match frequencies
Bioinformatics, September 1, 2007; 23(17): 2210 - 2217.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
J. Adachi, C. Kumar, Y. Zhang, and M. Mann
In-depth Analysis of the Adipocyte Proteome by Mass Spectrometry and Bioinformatics
Mol. Cell. Proteomics, July 1, 2007; 6(7): 1257 - 1273.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
T. S. Price, M. B. Lucitt, W. Wu, D. J. Austin, A. Pizarro, A. K. Yocum, I. A. Blair, G. A. FitzGerald, and T. Grosser
EBP, a Program for Protein Identification Using Multiple Tandem Mass Spectrometry Datasets
Mol. Cell. Proteomics, March 1, 2007; 6(3): 527 - 536.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
R. P. Munton, R. Tweedie-Cullen, M. Livingstone-Zatchej, F. Weinandy, M. Waidelich, D. Longo, P. Gehrig, F. Potthast, D. Rutishauser, B. Gerrits, et al.
Qualitative and Quantitative Analyses of Protein Phosphorylation in Naive and Stimulated Mouse Synaptosomal Preparations
Mol. Cell. Proteomics, February 1, 2007; 6(2): 283 - 293.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
S. Sun, K. Meyer-Arendt, B. Eichelberger, R. Brown, C.-Y. Yen, W. M. Old, K. Pierce, K. J. Cios, N. G. Ahn, and K. A. Resing
Improved Validation of Peptide MS/MS Assignments Using Spectral Intensity Prediction
Mol. Cell. Proteomics, January 1, 2007; 6(1): 1 - 17.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
G.-J. C. M. van den Bemd, J. Krijgsveld, T. M. Luider, A. L. van Rijswijk, J. A. A. Demmers, and G. Jenster
Mass Spectrometric Identification of Human Prostate Cancer-derived Proteins in Serum of Xenograft-bearing Mice
Mol. Cell. Proteomics, October 1, 2006; 5(10): 1830 - 1839.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
B. Domon and R. Aebersold
Challenges and Opportunities in Proteomics Data Analysis
Mol. Cell. Proteomics, October 1, 2006; 5(10): 1921 - 1926.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
W. Haas, B. K. Faherty, S. A. Gerber, J. E. Elias, S. A. Beausoleil, C. E. Bakalarski, X. Li, J. Villen, and S. P. Gygi
Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics
Mol. Cell. Proteomics, July 1, 2006; 5(7): 1326 - 1337.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
Q. C. Ru, L. A. Zhu, J. Silberman, and C. D. Shriver
Label-free Semiquantitative Peptide Feature Profiling of Human Breast Cancer and Breast Disease Sera via Two-dimensional Liquid Chromatography-Mass Spectrometry
Mol. Cell. Proteomics, June 1, 2006; 5(6): 1095 - 1104.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
A. I. Nesvizhskii, F. F. Roos, J. Grossmann, M. Vogelzang, J. S. Eddes, W. Gruissem, S. Baginsky, and R. Aebersold
Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data: Toward More Efficient Identification of Post-translational Modifications, Sequence Polymorphisms, and Novel Peptides
Mol. Cell. Proteomics, April 1, 2006; 5(4): 652 - 670.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
 All ASBMB Journals   Journal of Biological Chemistry 
 Journal of Lipid Research   ASBMB Today 
Copyright © 2005 by the American Society for Biochemistry and Molecular Biology.
Advertisement
spacer
Advertisement
Advertisement