Feature Request Sequence Dependent Precursor Charges

Feature Request Sequence Dependent Precursor Charges roman sakson  2019-06-13

Hello everyone,

first of all, thanks again for the amazing piece of software that continues to be the highlight of my research days!

I work in a core facility, where we routinely develop MRM assays from crude synthetic standards without much prior knowledge, this means that for the first runs we have to "guess" the precursor charge state as well as suitable transitions based on common MS sense for relatively long target lists. In our experience, doubly charged precursor ions work best for tryptic peptides of average length, therefore this is the standard transition setting. However, if the sequence contains histidine, normally the more intensive precursor is triply charged. Is it possible to specify in the filter settings or elsewhere, that precursors should be doubly charged, unless there is a particular amino acid present in the sequence?

Thanks a lot in advance for your time!

Roman (Heidelberg, Germany)

Tobi responded:  2019-06-17

Hello all,

if possible I would like to add something which has also been mentioned before. It would be nice to have an automated charge state refinement. The idea would be (for standard peptides etc.) to build chromatograms for charge states 2+ to X+, manually check and correct peak picking, and with a few clicks to filter the target list to have only the most intense charge state left over. Removing the need of having to make deletions for every single peptide would be a big plus.

Best regards,