Hi Will, Glad you got this to work! A potentially quicker solution is to enter those extra flags in the "additional options" box in Petunia:
[image: image.png] You can find a full set of available options at the Proteowizard msconvert info page: https://proteowizard.sourceforge.io/tools/msconvert.html At some point we'll add more options to this page as well. Cheers, --Luis On Fri, Apr 7, 2023 at 10:55 AM Will Comstock <wc...@cornell.edu> wrote: > Okay I got it to work. For the record, my solution was the following: > > > 1. Rather than use the msConvert packaged with the TPP, I downloaded > it separately from ProteoWizard. > 2. I converted my RAW file with the following parameters: > > > - [image: SIM_msConvert.PNG] > - (I am not sure if "SRM as spectra" is required, but "SIM as spectra" > was key as all my MS1 scans were classified as SIM-MS scans) > > 3. I then searched the resulting mzML file as normal. > > Thanks again, Jimmy! > -Will > > On Friday, April 7, 2023 at 1:04:44 PM UTC-4 Will Comstock wrote: > >> 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 <jke...@gmail.com> 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 <wc...@cornell.edu> 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 spctools-discu...@googlegroups.com. >>>> 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 >>> spctools-discu...@googlegroups.com. >>> 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 spctools-discuss+unsubscr...@googlegroups.com. > To view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/f5a47108-95f1-4f8b-a44b-ca48a6c6cdafn%40googlegroups.com > <https://groups.google.com/d/msgid/spctools-discuss/f5a47108-95f1-4f8b-a44b-ca48a6c6cdafn%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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CACyS9bp_tDqKGyz1kyQYwv8nAWiixriYHtmM6b9KVBFP1Sargw%40mail.gmail.com.
