1 Generalities

Spectral counts quantitation: this variant is based on the counting of the mass spectra that have allowed the identification of a given protein. It has the advantage of being a label-free quantitative technique, but it is also too rough to be considered a “robust and precise” technique.

Area under the curve quantitation: this variant is based on the integration of the ion current that can be extracted from the mass data (“extracted ion current”, or XIC) for the precursors ions that, upon fragmentation, led to the protein identification. By integrating the XICs for all the peptide precursors that identified a given protein, the software can estimate the abundance of that specific protein. The software thus needs to be able to extract the ion current for all the precursor ions in the MS spectra, when these ions were fragmented and allowed identifying peptides that in turn identified proteins. This is the process that MassChroQ implements, which is why it is called Mass Chromatogram Quantification, with Chromatogram referring to the extracted ion current (XIC) chromatogram used to assign an intensity value to the peptide ion that was fragmented.

X!TandemPipeline can produce that file and has a MassChroQ configuration interface that is well documented in the user manual. The masschroqml file contains all the data required for the MassChroQ operation.

For scientists not using X!TandemPipeline for their proteomics projects, it is possible to craft the masschroqml file starting from a rudimentary file and by pointing MassChroQ to a tsv file (a tab-separated values file) containing the data required by MassChroQ. A typical file is shown in Figure 1.1, “The peptide list file in tsv format”.

Note

It is important that the mh column be filled-in with the calculated [M+H]⁺ ion mass. The charge column (z column) represents the actual charge of the precursor peptide ion.

Then do this: FIXME