The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling
Abstract
Label‐free quantification of high mass resolution LC‐MS data has emerged as a promising technology for proteome analysis. Computational methods are required for the accurate extraction of peptide signals from LC‐MS data and the tracking of these features across the measurements of different samples. We present here an open source software tool, SuperHirn, that comprises a set of modules to process LC‐MS data acquired on a high resolution mass spectrometer. The program includes newly developed functionalities to analyze LC‐MS data such as feature extraction and quantification, LC‐MS similarity analysis, LC‐MS alignment of multiple datasets, and intensity normalization. These program routines extract profiles of measured features and comprise tools for clustering and classification analysis of the profiles. SuperHirn was applied in an MS1‐based profiling approach to a benchmark LC‐MS dataset of complex protein mixtures with defined concentration changes. We show that the program automatically detects profiling trends in an unsupervised manner and is able to associate proteins to their correct theoretical dilution profile.
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Cites
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Hastie, T., Friedman, J., & Tibshirani, R. (2001) · Springer Series in Statistics · doi:10.1007/978-0-387-21606-5 · Cited by 24,162
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Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Self-citationOng, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574
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Proteomic characterization of the human centrosome by protein correlation profiling
Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P., Nigg, E. A., & Mann, M. (2003) · Nature · doi:10.1038/nature02166 · Cited by 1,319
Cited by
Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.031591 · Cited by 5,180
Protein Analysis by Shotgun/Bottom-up Proteomics
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491
Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present
Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801
Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins
Wollscheid, B., Bausch-Fluck, D., Henderson, C., O'Brien, R., Bibel, M., Schiess, R., Aebersold, R., & Watts, J. D. (2009) · Nature Biotechnology · doi:10.1038/nbt.1532 · Cited by 547
Self-citationCollins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00249-5 · Cited by 576
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Metadata
- Authors
- Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M., Vitek, O., Aebersold, R., & Müller, M.
- Venue
- PROTEOMICS
- Publisher
- Wiley
- Published
- 2007-10
- Volume
- 7
- Issue
- 19
- Pages
- 3470-3480
- ISSN
- 1615-9853 (ISSN-L)
- 1615-9861
- OpenAlex
- W2158447287
- Cited by
- 308
- References
- 6
- FWCI
- 14.09
- Type
- journal article
- Language
- en
- Open access
- closed
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- Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M., Vitek, O., Aebersold, R., & Müller, M. (2007). SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling. PROTEOMICS. https://doi.org/10.1002/pmic.200700057
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