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Single amino acid substitutions in mascot error tolerant search

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Single amino acid substitutions in mascot error tolerant search michelle dubuke  2018-05-21 09:28
 

Hi,

I am working on a peptide-based project with single amino acid substitutions at specified locations in the sequence. I am able to build a fasta file that contains all of the possible peptide sequences and do the analysis that way, but an error-tolerant search in mascot is faster and allows me to look for "off target" amino acid substitutions. I updated to skyline-daily to get the error tolerant searches to populate properly, but it appears that the single amino acid substitutions are not pulling from unimod like the rest of the options/chemical modifications are for that data.

Is there any reason why the amino acid changes wouldn't be included in skyline during error tolerant searching?

Thanks,
Michelle Dubuke
UMass Medical School
 
 
Kaipo Tamura responded:  2018-05-21 11:45

Hi Michelle,
Would you mind sharing your Mascot file so that I can reproduce and fix this issue? You may upload it at https://skyline.ms/files.url or email it to me directly if you prefer.

Thanks,
Kaipo
 
michelle dubuke responded:  2018-05-22 13:55

Hi Kaipo,

Unfortunately, this is for a client under an NDA and I can't share the results of the mascot file; would you need more beyond the header?

Thanks,
Michelle
 
Brendan MacLean responded:  2018-05-22 14:00

Maybe you could just run a similar search on unimportant data and send us the Mascot .dat file for that? It is more that we need a good example of what your configuration produces than that we need any specific file.