The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data
Abstract
Over the past decade, a series of experimental strategies for mass spectrometry based quantitative proteomics and corresponding computational methodology for the processing of the resulting data have been generated. We provide here an overview of the main quantification principles and available software solutions for the analysis of data generated by liquid chromatography coupled to mass spectrometry (LC-MS). Three conceptually different methods to perform quantitative LC-MS experiments have been introduced. In the first, quantification is achieved by spectral counting, in the second via differential stable isotopic labeling, and in the third by using the ion current in label-free LC-MS measurements. We discuss here advantages and challenges of each quantification approach and assess available software solutions with respect to their instrument compatibility and processing functionality. This review therefore serves as a starting point for researchers to choose an appropriate software solution for quantitative proteomic experiments based on their experimental and analytical requirements.
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Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
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Systems Biology and New Technologies Enable Predictive and Preventative Medicine
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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
Correlation of mRNA and protein in complex biological samples
Maier, T., Güell, M., & Serrano, L. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.036 · Cited by 1,802
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
Proteomics by Mass Spectrometry: Approaches, Advances, and Applications
Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-061008-124934 · Cited by 1,078
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
Metadata
- Authors
- Mueller, L. N., Brusniak, M.-Y., Mani, D. R., & Aebersold, R.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2008-01-01
- Volume
- 7
- Issue
- 1
- Pages
- 51-61
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- OpenAlex
- W2038249420
- Cited by
- 449
- References
- 5
- FWCI
- 31.25
- Type
- journal article
- Language
- en
- Open access
- closed
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