The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
PASSEL: The PeptideAtlas SRM experiment library
Open accessAbstract
Public repositories for proteomics data have accelerated proteomics research by enabling more efficient cross‐analyses of datasets, supporting the creation of protein and peptide compendia of experimental results, supporting the development and testing of new software tools, and facilitating the manuscript review process. The repositories available to date have been designed to accommodate either shotgun experiments or generic proteomic data files. Here, we describe a new kind of proteomic data repository for the collection and representation of data from selected reaction monitoring (SRM) measurements. The P eptide A tlas SRM E xperiment L ibrary (PASSEL) allows researchers to easily submit proteomic data sets generated by SRM. The raw data are automatically processed in a uniform manner and the results are stored in a database, where they may be downloaded or browsed via a web interface that includes a chromatogram viewer. PASSEL enables cross‐analysis of SRM data, supports optimization of SRM data collection, and facilitates the review process of SRM data. Further, PASSEL will help in the assessment of proteotypic peptide performance in a wide array of samples containing the same peptide, as well as across multiple experimental protocols.
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Cites
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationDesiere, F. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj040 · Cited by 910
mProphet: automated data processing and statistical validation for large-scale SRM experiments
Reiter, L., Rinner, O., Picotti, P., Hüttenhain, R., Beck, M., Brusniak, M.-Y., Hengartner, M. O., & Aebersold, R. (2011) · Nature Methods · doi:10.1038/nmeth.1584 · Cited by 532
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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
Perez-Riverol, Y., Bai, J., Bandla, C., García-Seisdedos, D., Hewapathirana, S., Kamatchinathan, S., Kundu, D. J., Prakash, A., Frericks-Zipper, A., Eisenacher, M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1038 · Cited by 6,125
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-citationThe Proteomics Identifications (PRIDE) database and associated tools: status in 2013
Vizcaíno, J. A., Côté, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1262 · Cited by 1,918
Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., & Coon, J. J. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.020131 · Cited by 1,288
The ProteomeXchange consortium at 10 years: 2023 update
Deutsch, E. W., Bandeira, N., Perez-Riverol, Y., Sharma, V., Carver, J. J., Mendoza, L., Kundu, D. J., Wang, S., Bandla, C., Kamatchinathan, S., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1040 · Cited by 819
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Metadata
- Authors
- Farrah, T., Deutsch, E. W., Kreisberg, R., Sun, Z., Campbell, D. S., Mendoza, L., Kusebauch, U., Brusniak, M., Hüttenhain, R., Schiess, R., Selevsek, N., Aebersold, R., & Moritz, R. L.
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2012-04
- Volume
- 12
- Issue
- 8
- Pages
- 1170-1175
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- OpenAlex
- W2167089719
- Cited by
- 207
- References
- 3
- FWCI
- 9.84
- Type
- journal article
- Language
- en
- Open access
- green
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- Farrah, T., Deutsch, E. W., Kreisberg, R., Sun, Z., Campbell, D. S., Mendoza, L., Kusebauch, U., Brusniak, M., Hüttenhain, R., Schiess, R., Selevsek, N., Aebersold, R., & Moritz, R. L. (2012). PASSEL: The PeptideAtlas SRM experiment library. PROTEOMICS. https://doi.org/10.1002/pmic.201100515
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