Comprehensive support for quantitation
One of the major new features in the current release of Mascot is support for quantitation. This is still work in progress. Our goal is to support all of the popular methodologies.
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Quantitation - Overview
Protocol
reporter precursor multiplex (Neubert et. al.) replicate empai (Ishihama et. al.) average
Description
Specific reporter ion peaks within a single MS/MS spectrum Extracted ion chromatograms for related precursors within a single dataset Pairs of sequence ion fragment peaks within a single MS/MS spectrum Extracted ion chromatograms for identical precursors across two or more datasets Protein coverage in a database search result Extracted ion chromatograms for selected peptides per protein within a single dataset
Examples
iTRAQ, ExacTag, TMT ICAT, SILAC, 18O, ICPL, AQUA, Metabolic SILAC,
18O
Label-free
: Quantitation
2007 Matrix Science
To make this task manageable, we have classified the various approaches into a limited number of protocols. So far, we have identified 6 distinct protocols. If anyone can see a method that doesn't fit to one of these, we'd be very grateful for details. Reporter is quantitation based on the relative intensities of fragment peaks at fixed m/z values within an MS/MS spectrum. For example, iTRAQ or Tandem Mass Tags Precursor is quantitation based on the relative intensities of extracted ion chromatograms (XICs) for precursors within a single data set. This is by far the most widely used approach, which can be used with any chemistry that creates a precursor mass shift. For example, 18O, AQUA, ICAT, ICPL, Metabolic, SILAC, etc., etc. Multiplex is quantitation based on the relative intensities of sequence ion fragment peaks within an MS/MS spectrum. This is a novel approach, which can be used with any chemistry that labels one peptide terminus, creating a small mass shift, such as 18O or SILAC under certain conditions. Replicate is 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. emPAI is quantitation for the proteins in a mixture based on protein coverage by the peptide matches in a database search result. Average is quantitation for the proteins in a mixture based on the application of a rule to the intensities of extracted ion chromatograms (XICs) for the peptide matches in a database search result. For example, the average intensity for the three strongest peptide matches per protein The rows with a blue background are the protocols that are fully implemented in Mascot 2.2

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