The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.
MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics
Open accessAbstract
Mass spectrometry-based proteomics critically depends on algorithms for data interpretation. A current bottleneck in the rapid advance of proteomics technology is the closed nature and slow development cycle of vendor-supplied software solutions. We have created an open source software environment, called MSQuant, which allows visualization and validation of peptide identification results directly on the raw mass spectrometric data. MSQuant iteratively recalibrates MS data thereby significantly increasing mass accuracy leading to fewer false positive peptide identifications. Algorithms to increase data quality include an MS(3) score for peptide identification and a post-translational modification (PTM) score that determines the probability that a modification such as phosphorylation is placed at a specific residue in an identified peptide. MSQuant supports relative protein quantitation based on precursor ion intensities, including element labels (e.g., (15)N), residue labels (e.g., SILAC and ICAT), termini labels (e.g., (18)O), functional group labels (e.g., mTRAQ), and label-free ion intensity approaches. MSQuant is available, including an installer and supporting scripts, at http://msquant.sourceforge.net .
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Cites
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
Self-citationBioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,172
Mass spectrometry-based proteomics
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
Self-citationQuantitative analysis of complex protein mixtures using isotope-coded affinity tags
Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., & Mann, M. (2006) · Cell · doi:10.1016/j.cell.2006.09.026 · Cited by 3,499
Self-citationBeausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577
Mass spectrometry–based proteomics turns quantitative
Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572
Self-citationOlsen, J. V., de Godoy, L. M. F., Li, G., Macek, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500030-mcp200 · Cited by 1,510
Self-citationLarge-scale characterization of HeLa cell nuclear phosphoproteins
Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., Villén, J., Li, J., Cohn, M. A., Cantley, L. C., & Gygi, S. P. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404720101 · Cited by 1,375
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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
Shimazu, T., Hirschey, M. D., Hua, L., Dittenhafer-Reed, K. E., Schwer, B., Lombard, D. B., Li, Y., Bunkenborg, J., Alt, F. W., Denu, J. M., et al. (2010) · Cell Metabolism · doi:10.1016/j.cmet.2010.11.003 · Cited by 484
Self-citationBioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Chen, C., Hou, J., Tanner, J. J., & Cheng, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082873 · Cited by 280
Catch me if you can: Mass spectrometry‐based phosphoproteomics and quantification strategies
Eyrich, B., Sickmann, A., & Zahedi, R. P. (2011) · PROTEOMICS · doi:10.1002/pmic.201000489 · Cited by 104
Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy
Zimmermann, A. C., Zarei, M., Eiselein, S., & Dengjel, J. (2010) · Autophagy · doi:10.4161/auto.6.8.12786 · Cited by 28
Metadata
- Authors
- Mortensen, P., Gouw, J. W., Olsen, J. V., Ong, S.-E., Rigbolt, K. T. G., Bunkenborg, J., Cox, J., Foster, L. J., Heck, A. J. R., Blagoev, B., Andersen, J. S., & Mann, M.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-11-18
- Volume
- 9
- Issue
- 1
- Pages
- 393-403
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2037334311
- Cited by
- 254
- References
- 41
- FWCI
- 20.96
- Type
- journal article
- Language
- en
- Open access
- green
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