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VIPER: an advanced software package to support high-throughput LC-MS peptide identification
Open accessAbstract
Summary: The accurate mass and time (AMT) tag approach is used for analysis of large scale experiments by combining information generated over multiple datasets and instrument types. The VIPER software package is one of the key components of the data processing pipeline and implements automated algorithms to discover LC-MS features, align and match these LC-MS features to a database of peptides previously identified in LC-MS/MS analyses, and identify and quantify pairs of isotopically labeled peptides. Availability: VIPER may be downloaded free of charge at http://ncrr.pnl.gov/software/ Contact: rds@pnl.gov or proteomics@pnl.gov Supplementary information: Supplementary data are available at Bioinformatics online.
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Cited by
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Comparative analysis of proteome and transcriptome variation in mouse
Ghazalpour, A., Bennett, B., Petyuk, V. A., Orozco, L., Hagopian, R., Mungrue, I. N., Farber, C. R., Sinsheimer, J., Kang, H. M., Furlotte, N., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1001393 · Cited by 624
“LC-MS datasets were analyzed by in-house software VIPER [38] that detected features in mass – elution time space and assigned them to peptides in AMT tag database as described elsewhere [39,40].”
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Zhang, Z., Wu, S., Stenoien, D. L., & Paša-Tolić, L. (2014) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071213-020216 · Cited by 323
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
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Metadata
- Authors
- Monroe, M. E., Tolić, N., Jaitly, N., Shaw, J. L., Adkins, J. N., & Smith, R. D.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-06-01
- Volume
- 23
- Issue
- 15
- Pages
- 2021-2023
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2124114991
- Cited by
- 189
- References
- 0
- FWCI
- 8.86
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Monroe, M. E., Tolić, N., Jaitly, N., Shaw, J. L., Adkins, J. N., & Smith, R. D. (2007). VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics. https://doi.org/10.1093/bioinformatics/btm281
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