Good catch, I will try to redo the RAW conversion to include my MS1 scans. Thanks Jimmy!
-Will On Fri, Apr 7, 2023 at 12:50 PM Jimmy Eng <[email protected]> wrote: > 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 a topic in the > Google Groups "spctools-discuss" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/spctools-discuss/6-Q5KuqumMQ/unsubscribe > . > To unsubscribe from this group and all its topics, 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 > <https://groups.google.com/d/msgid/spctools-discuss/CAJqD6EOFuHubneYYdcL0Z1cUqiJRi%3Ds%2B%2BrmjXgz9otBT5zDMtg%40mail.gmail.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/CALJ7d9ytOk%2BPCPZU2Qw3PLZ_qq3b2QqtwBkYs3unMS96SMtFgQ%40mail.gmail.com.
