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 <[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
>>>
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