System.IO.IOException: ERROR: Illegal character p found in sequence ..... jason a macgurn  2019-04-15


I am using skyline with MS1 full scan filtering on data acquired from a Q Exactive and searched on MaxQuant. I am using Skyline to inspect peptides (especially phosphopeptides) and validate quantification from SILAC labeling.

I had been using a very nice workflow (based on the MS1 full scan filtering tutorial) that was perfect for our application. But recently, I had some computer problems which forced me to install the latest versions of both MaxQuant and Skyline, and now whenever I try to set up the filtering on my data I receive the following error:

"ERROR: Illegal character p found in sequence AAGpSGESpTPER (line 13)"
(detailed error info in the attached text file)

I only get this error when I attempt to filter data generated with my new version of MaxQuant - if I filter analysis from the old version, there are no errors.

My interpretation is that Skyline doesn't like something about the way MaxQuant is formatting the msms.txt output file (phosphopeptides specifically?), so it chokes on it. I figure I either need to re-format the msms.txt output file or adjust some setting for the input on Skyline. Has anyone else encountered this problem? Is there a fix or workaround?
Thanks in advance for any help / suggestions - I am eager to get back to using Skyline for analysis of some of my data!

Nick Shulman responded:  2019-04-15
Can you send us your files? It sounds like we will need the msms.txt and maybe the mqpar.xml and modifications.xml if you have them.

If those files are less than 50MB, you can attach them to this support request.
Otherwise you can upload them here:

I am not the expert on our MaxQuant support, but it sounds like we are going to need to do some work to support this new version of MaxQuant.
-- Nick
jason a macgurn responded:  2019-04-15
Hi Nick,
Thanks for the rapid response!
Attached is an example msms.txt output and the mqpar.xml file from the new MaxQuant. I don't see a modifications.xml files (is that a normal MaxQuant output?) but I am including an output file titled modificationSpecificPeptides. (Not sure if its the same thing.)
Let me know if any additional files would be helpful. (e.g., I can upload older msms.txt files (from the previous version of MaxQuant) that do work well in skyline for comparison.......)
I hope this is helpful - thanks so much for your efforts!
lparsons responded:  2019-04-16

Just wanted to point out that we've been going around on this matter for a while now. I raised it on the MaxQuant forum a while back (!searchin/maxquant-list/skyline|sort:date/maxquant-list/f3Shf9-oBxU/DhQGSBe2GAAJ ) and the best we could figure out at the time was to edit the msms.txt file before importing it in Skyline.

If you change every "pS" in msms.txt to "S(ph)", the file will import without error. The same applies to pT and pY. It's not a pretty solution but it does work.
jason a macgurn responded:  2019-04-17
Thank you very much for your solution - very grateful!
matt.chambers42 responded:  2019-04-29
I've just committed a fix for this, it should be in the next Skyline-daily.