MS1 Quantification

As a discussion starter...

I have decided to rework N14N15 package. After thinking a bit it is not hard to realize that there are a lot of steps in N15/N14 ratio quantitation overlap with other MS1-based approaches. In particular label-free approach that uses area under the chromatographic curve as an abundance measure. Here are some steps/issues common across any MS1-based quantification approach.

• How do we store list of species to be quantified? I can add specifications what should be in such a container.
• Extract appropriate region of LC-MS dataset to work with. The interface is mzR. The remained issue is how to appropriately define the area of interest.
• Extraction of ion chromatogram.
• Conversion of peptide sequence to elemental composition. BRAIN::getAtomsFromSeq is something like that, but does not handle modifications (even the must have one - cysteine alkylation). Further problem is that, say in N15/N14 approach, some N atom are N15 enrichment, but some (the ones from iodoacetamide) have natural isotopic distribution. I have only ugly hacks that deal with this situation (by introducing a different type of N called as X). The situation should be similarly difficult for C13 metabolic labeling experiments.
• Generation of isotopic envelops is nicely handled by Rdisop and BRAIN.
• Other steps can be specific to MS1 approach be that label-free, N15/N14, C13/C12, SILAC or O18/O16.