Will, XPRESS extracts precursor intensities from MS1 scans and your mzXML file contains only MS/MS scans. So that's why XPRESS is failing because it's expecting to parse MS1 scans which aren't present in this file.
Jimmy On Fri, Apr 7, 2023 at 8:57 AM Will Comstock <[email protected]> wrote: > Hi all, > > I'm trying to use tSIM-ddMS2 to identify specific peptides in my sample, > but I also want SILAC quantification of those peptides using XPRESS. I've > made sure the MS1 isolation window is wide enough to see both Light and > Heavy peptide peaks for everything in my inclusion list (30 daltons, so my > heavy peptides which are +8 or +10 are detected). However, when I search > with Comet and XPRESS, there is no quantitative ratio provided, just -1.0. > XPRESS appears to be looking in the wrong place for the light and heavy > peptides, but I am not sure why or how to redirect it to the right parts of > my MS1 spectra. If I look at the precursor scans manually via QualBrowser, > both peaks are definitely being detected. > > Has anyone here tried using XPRESS to do SILAC quantitation in targeted > runs before? > > > Here is a folder with my data, search parameters, and database just in > case. > > https://drive.google.com/drive/folders/1142YHaxB1RC6HMcfuy_MdEN8T-sSLDSl?usp=sharing > > Thanks! > -Will > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EOFuHubneYYdcL0Z1cUqiJRi%3Ds%2B%2BrmjXgz9otBT5zDMtg%40mail.gmail.com.
