The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
Probability-Based Evaluation of Peptide and Protein Identifications from Tandem Mass Spectrometry and SEQUEST Analysis: The Human Proteome
Abstract
Large-scale protein identifications from highly complex protein mixtures have recently been achieved using multidimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) and subsequent database searching with algorithms such as SEQUEST. Here, we describe a probability-based evaluation of false positive rates associated with peptide identifications from three different human proteome samples. Peptides from human plasma, human mammary epithelial cell (HMEC) lysate, and human hepatocyte (Huh)-7.5 cell lysate were separated by strong cation exchange (SCX) chromatography coupled offline with reversed-phase capillary LC-MS/MS analyses. The MS/MS spectra were first analyzed by SEQUEST, searching independently against both normal and sequence-reversed human protein databases, and the false positive rates of peptide identifications for the three proteome samples were then analyzed and compared. The observed false positive rates of peptide identifications for human plasma were significantly higher than those for the human cell lines when identical filtering criteria were used, suggesting that the false positive rates are significantly dependent on sample characteristics, particularly the number of proteins found within the detectable dynamic range. Two new sets of filtering criteria are proposed for human plasma and human cell lines, respectively, to provide an overall confidence of >95% for peptide identifications. The new criteria were compared, using a normalized elution time (NET) criterion (Petritis et al. Anal. Chem. 2003, 75, 1039-1048), with previously published criteria (Washburn et al. Nat. Biotechnol. 2001, 19, 242-247). The results demonstrate that the present criteria provide significantly higher levels of confidence for peptide identifications from mammalian proteomes without greatly decreasing the number of identifications.
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Perkins, D. N., Pappin, D. J. C., Creasy, D. M., & Cottrell, J. S. (1999) · Electrophoresis · doi:10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2 · Cited by 8,203
Keller, A., Nesvizhskii, A. I., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,830
A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry
Nesvizhskii, A. I., Keller, A., Kolker, E., & Aebersold, R. (2003) · Analytical Chemistry · doi:10.1021/ac0341261 · Cited by 4,809
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
Washburn, M. P., Wolters, D., & Yates, J. R. (2001) · Nature Biotechnology · doi:10.1038/85686 · Cited by 4,752
Anderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414
Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., & Gygi, S. P. (2003) · Journal of Proteome Research · doi:10.1021/pr025556v · Cited by 1,647
A proteomic view of the Plasmodium falciparum life cycle
Florens, L., Washburn, M. P., Raine, J. D., Anthony, R. M., Grainger, M., Haynes, J. D., Moch, J. K., Muster, N., Sacci, J. B., Tabb, D. L., et al. (2002) · Nature · doi:10.1038/nature01107 · Cited by 1,308
Highly Permissive Cell Lines for Subgenomic and Genomic Hepatitis C Virus RNA Replication
Blight, K. J., McKeating, J. A., & Rice, C. M. (2002) · Journal of Virology · doi:10.1128/jvi.76.24.13001-13014.2002 · Cited by 1,193
Anderson, N. L., Polanski, M., Pieper, R., Gatlin, T., Tirumalai, R. S., Conrads, T. P., Veenstra, T. D., Adkins, J. N., Pounds, J. G., Fagan, R., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300127-mcp200 · Cited by 1,006
Toward a Human Blood Serum Proteome
Adkins, J. N., Varnum, S. M., Auberry, K. J., Moore, R. J., Angell, N. H., Smith, R. D., Springer, D. L., & Pounds, J. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200066-mcp200 · Cited by 793
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Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W., Menon, R., Hermjakob, H., Apweiler, R., Haab, B. B., Simpson, R. J., Eddes, J. S., et al. (2005) · PROTEOMICS · doi:10.1002/pmic.200500358 · Cited by 787
Qian, W.-J., Kaleta, D. T., Petritis, B. O., Jiang, H., Liu, T., Zhang, X., Mottaz, H. M., Varnum, S. M., Camp, D. G., Huang, L., et al. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800008-mcp200 · Cited by 208
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Self-citationManes, N. P., Estep, R. D., Mottaz, H. M., Moore, R. J., Clauss, T. R. W., Monroe, M. E., Du, X., Adkins, J. N., Wong, S. W., & Smith, R. D. (2008) · Journal of Proteome Research · doi:10.1021/pr070432+ · Cited by 103
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The distinct proteome of placental malaria parasites
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Metadata
- Authors
- Qian, W.-J., Liu, T., Monroe, M. E., Strittmatter, E. F., Jacobs, J. M., Kangas, L. J., Petritis, K., Camp, D. G., & Smith, R. D.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2004-12-13
- Volume
- 4
- Issue
- 1
- Pages
- 53-62
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2089492568
- Cited by
- 317
- References
- 24
- FWCI
- 13.50
- Type
- journal article
- Language
- en
- Open access
- closed
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