The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
PeptideShaker enables reanalysis of MS-derived proteomics data sets
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
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925
Goecks, J., Nekrutenko, A., Taylor, J., & The Galaxy Team (2010) · Genome Biology · doi:10.1186/gb-2010-11-8-r86 · Cited by 3,453
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
Vizcaíno, J. A., Deutsch, E. W., Wang, R., Csordas, A., Reisinger, F., Ríos, D., Dianes, J. A., Sun, Z., Farrah, T., Bandeira, N., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2839 · Cited by 2,729
Self-citationInterpretation of Shotgun Proteomic Data
Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025
PRIDE: The proteomics identifications database
Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., & Apweiler, R. (2005) · PROTEOMICS · doi:10.1002/pmic.200401303 · Cited by 594
Self-citationNesvizhskii, A. I. (2010) · Journal of Proteomics · doi:10.1016/j.jprot.2010.08.009 · Cited by 536
SearchGUI: An open‐source graphical user interface for simultaneous OMSSA and X!Tandem searches
Vaudel, M., Barsnes, H., Berven, F. S., Sickmann, A., & Martens, L. (2011) · PROTEOMICS · doi:10.1002/pmic.201000595 · Cited by 356
Self-citationThe chromosome-centric human proteome project for cataloging proteins encoded in the genome
Paik, Y.-K., Jeong, S.-K., Omenn, G. S., Uhlen, M., Hanash, S., Cho, S. Y., Lee, H.-J., Na, K., Choi, E.-Y., Yan, F., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2152 · Cited by 288
The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S. J., Selley, J. N., Searle, B. C., Shofstahl, J., Seymour, S. L., et al. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014381 · Cited by 199
Combining Results of Multiple Search Engines in Proteomics
Shteynberg, D., Nesvizhskii, A. I., Moritz, R. L., & Deutsch, E. W. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r113.027797 · Cited by 187
Cited by
Philosopher: a versatile toolkit for shotgun proteomics data analysis
da Veiga Leprevost, F., Haynes, S. E., Avtonomov, D. M., Chang, H.-Y., Shanmugam, A. K., Mellacheruvu, D., Kong, A. T., & Nesvizhskii, A. I. (2020) · Nature Methods · doi:10.1038/s41592-020-0912-y · Cited by 632
Proline: an efficient and user-friendly software suite for large-scale proteomics
Bouyssié, D., Hesse, A.-M., Mouton-Barbosa, E., Rompais, M., Macron, C., Carapito, C., Gonzalez de Peredo, A., Couté, Y., Dupierris, V., Burel, A., et al. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa118 · Cited by 300
Proteome Discoverer—A Community Enhanced Data Processing Suite for Protein Informatics
Orsburn, B. C. (2021) · Proteomes · doi:10.3390/proteomes9010015 · Cited by 336
Reich, S., Nguyen, C. D. L., Has, C., Steltgens, S., Soni, H., Coman, C., Freyberg, M., Bichler, A., Seifert, N., Conrad, D., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16747-y · Cited by 90
Verbruggen, S., Ndah, E., Van Criekinge, W., Gessulat, S., Kuster, B., Wilhelm, M., Van Damme, P., & Menschaert, G. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra118.001218 · Cited by 45
Metadata
- Authors
- Vaudel, M., Burkhart, J. M., Zahedi, R. P., Oveland, E., Berven, F. S., Sickmann, A., Martens, L., & Barsnes, H.
- Venue
- Nature Biotechnology
- Published
- 2015-01
- Volume
- 33
- Issue
- 1
- Pages
- 22-24
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2029849110
- Cited by
- 522
- References
- 18
- FWCI
- 28.58
- 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: PeptideShaker enables reanalysis of MS-derived proteomics data sets. https://app.cochat.ai/papers/10.1038/nbt.3109
- The paper
- Vaudel, M., Burkhart, J. M., Zahedi, R. P., Oveland, E., Berven, F. S., Sickmann, A., Martens, L., & Barsnes, H. (2015). PeptideShaker enables reanalysis of MS-derived proteomics data sets. Nature Biotechnology. https://doi.org/10.1038/nbt.3109
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.
