The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome
Abstract
Highly complex protein mixtures can be directly analyzed after proteolysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this paper, we have utilized the combination of strong cation exchange (SCX) and reversed-phase (RP) chromatography to achieve two-dimensional separation prior to MS/MS. One milligram of whole yeast protein was proteolyzed and separated by SCX chromatography (2.1 mm i.d.) with fraction collection every minute during an 80-min elution. Eighty fractions were reduced in volume and then re-injected via an autosampler in an automated fashion using a vented-column (100 microm i.d.) approach for RP-LC-MS/MS analysis. More than 162,000 MS/MS spectra were collected with 26,815 matched to yeast peptides (7,537 unique peptides). A total of 1,504 yeast proteins were unambiguously identified in this single analysis. We present a comparison of this experiment with a previously published yeast proteome analysis by Yates and colleagues (Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol. 2001, 19, 242-7). In addition, we report an in-depth analysis of the false-positive rates associated with peptide identification using the Sequest algorithm and a reversed yeast protein database. New criteria are proposed to decrease false-positives to less than 1% and to greatly reduce the need for manual interpretation while permitting more proteins to be identified.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
High resolution two-dimensional electrophoresis of proteins.
O'Farrell, P. (1975) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)41496-8 · Cited by 19,246
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
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
Proteomics to study genes and genomes
Pandey, A., & Mann, M. (2000) · Nature · doi:10.1038/35015709 · Cited by 2,373
An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics
Wolters, D. A., Washburn, M. P., & Yates, J. R. (2001) · Analytical Chemistry · doi:10.1021/ac010617e · Cited by 1,819
The current state of two-dimensional electrophoresis with immobilized pH gradients
Görg, A., Obermaier, C., Boguth, G., Harder, A., Scheibe, B., Wildgruber, R., & Weiss, W. (2000) · Electrophoresis · doi:10.1002/(sici)1522-2683(20000401)21:6<1037::aid-elps1037>3.0.co;2-v · Cited by 1,515
Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags
Mann, M., & Wilm, M. (1994) · Analytical Chemistry · doi:10.1021/ac00096a002 · Cited by 1,468
Mass Spectrometry in Proteomics
Aebersold, R., & Goodlett, D. R. (2001) · Chemical Reviews · doi:10.1021/cr990076h · Cited by 1,238
Analysis of Proteins and Proteomes by Mass Spectrometry
Mann, M., Hendrickson, R. C., & Pandey, A. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.437 · Cited by 1,219
Clauser, K. R., Baker, P., & Burlingame, A. L. (1999) · Analytical Chemistry · doi:10.1021/ac9810516 · Cited by 1,093
Cited by
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Self-citationSemi-supervised learning for peptide identification from shotgun proteomics datasets
Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424
Correlation of mRNA and protein in complex biological samples
Maier, T., Güell, M., & Serrano, L. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.036 · Cited by 1,802
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733
Self-citation
Metadata
- Authors
- Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., & Gygi, S. P.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2002-10-15
- Volume
- 2
- Issue
- 1
- Pages
- 43-50
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2153132589
- Cited by
- 1,647
- References
- 19
- FWCI
- 37.50
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. https://app.cochat.ai/papers/10.1021/pr025556v
- The paper
- Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., & Gygi, S. P. (2003). Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. Journal of Proteome Research. https://doi.org/10.1021/pr025556v
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
