Journal
AMINO ACIDS
Volume 43, Issue 3, Pages 1087-1108Publisher
SPRINGER WIEN
DOI: 10.1007/s00726-012-1289-8
Keywords
LC-MS; Quantitative proteomics; Quantification software; Stable isotope labeling; Label-free
Categories
Funding
- PRIME-XS project [262067]
- European Union
- Netherlands Proteomics Centre, Netherlands Genomics Initiative
- Netherlands Bioinformatics Centre
- Centre for Biomedical Genetics
- NIH [NCRR RR001614, RR019934]
- MRC
- CR-UK
- BBSRC
- Barts and the London Charity
- BBSRC [BB/G015023/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/G015023/1] Funding Source: researchfish
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Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often considered the main bottleneck for proteomics development. This review highlights important issues that directly impact the effectiveness of proteomic quantitation and educates software developers and end-users on available computational solutions to correct for the occurrence of these factors. Potential sources of errors specific for stable isotope-based methods or label-free approaches are explicitly outlined. The overall aim focuses on a generic proteomic workflow.
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