Quantitation: Replicate protocol
The replicate protocol is used for label-free quantitation based on the relative
intensities of extracted ion chromatograms (XICs) for precursors in multiple
data sets aligned using mass and elution time.
This protocol requires information from the raw data file that is not
present in the peak list, so the quantitation report is
generated in Mascot Distiller, which has access to both the Mascot
search results and the raw data.
The accuracy of this protocol is highly dependent on good mass accuracy and reproducible
chromatography, so it is not surprising that instrument manufacturers have played a
major part in its development. In no particular order, a few key publications are:
- Wang, W. X., et al.,
Quantification of proteins and metabolites by mass spectrometry without isotopic
labeling or spiked standards, Analytical Chemistry 75 4818-4826 (2003)
- Chelius, D., et al.,
Global protein identification and quantification technology using two-dimensional
liquid chromatography nanospray mass spectrometry, Analytical Chemistry 75
6658-6665 (2003)
- Radulovic, D.,
et al., Informatics platform for global proteomic profiling and biomarker discovery
using liquid chromatography-tandem mass spectrometry, Molecular & Cellular Proteomics
3 984-997 (2004)
- Silva, J. C., et al.,
Quantitative proteomic analysis by accurate mass retention time pairs, Analytical
Chemistry 77 2187-2200 (2005)
- Hughes, M. A., et al.,
Quantitative proteomic analysis of drug-induced changes in mycobacteria, Journal of
Proteome Research 5 54-63 (2006)
More detailed information about quantitation reports for the replicate protocol
will be available as soon as the Mascot Distiller Quantitation Toolbox is released.
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