Using SProCoP with SRM data?

SProCoP
Using SProCoP with SRM data? andre  2014-08-17
 
Hi Michael,

I tried using SProCoP with an SRM data set (two traces for the analyte and one trace for the internal standard) acquired on an ABI Sciex 5500 QTRAP and couldn't make it work; when checking the SProCoP input file I noticed that the mass error column shows N/A entries. Is this a general issue with SRM data?

Best regards,
Andre
 
 
Michael responded:  2014-08-17
Hi Andre

Thank-you for your note. Skyline does not extract mma for low resolving power instruments like the qtrap. That's why you have a column of NAs. So try just leaving the mma and rp checkboxes blank and see if it runs this time. Also sprocop will only accept a single precursor per peptide. If this is not working I will be happy to take a look at the document myself

Thanks
Michael
 
andre responded:  2014-08-18
Hi Michael,

thanks for your quick response. However, when starting SProCoP the only checkbox to select is "Using high resolution instrumen" (which I had not selected); also, there is only one precursor per peptide (although in a light and heavy version).
So, it would be great if you could have a look at my document.

Thanks,
Andre
 
Michael responded:  2014-08-27
Hi Andre -

 Still looking into this - Sorry for the delay

Michael
 
Michael responded:  2014-09-07
Hi Andre -

 This is a bug - we will fix it - Thankyou for reporting it - Ill let you know when an updated version is out.

My apologies
Michael
 
brian flatley responded:  2014-11-28
Hi Michael,

I am having the same problem as Andre, I am trying to monitor 8 peptides across a large number of batches, but I fail to get SProCop to run currently. I have NAs in the average PPM mass error column.

Any help would be great,

Cheers,

Brian
 
Michael responded:  2014-11-28
Hi Brian -

 Thank you for your note. Would you mind sharing the zip file or part of the file? You can send it msberema@ncsu.edu.

Thanks
Michael
 
Michael responded:  2014-12-03
Hi Brian -

I updated the code so that your file now runs. But I deleted one of your peptides that had several NAs with fwhm. But the fact its SRM data does not matter now. Please let me know if this works for you. Just have to download the new version.

Sorry for the delay

Michael