Cannot create a spectral library from mzID generated by MM

[yishai99]

Hi, when trying to import search results from MetaMorpheus into Skyline or trying to create a library in Skyline using the mzID files generated by MM, we get an error. The Skyline team says its a none standard mzID format. Can you look into it? Thanks,

Yishai

[trishorts]

Right now we're working on a spectral library writer in MetaMorpheus. We should at least have something to test out this week. we'll leave this open and let you know. It will be .msp format. I hope that is okay. I don't know how to right the dlib format.

I think Rob figured out how to do spectral libraries with MM output in skyline. I'll ask him and see if we can explain it. I think it probably has to do with the modifications if memory serves.

[rmillikin]

I will copy+paste my response to an email from another user that had similar issues – can you try this solution and see if it works out for you? I will update this page https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Import-Results-Into-Skyline w/ this info also.

Thanks for your patience. I was able to get our .mzID file imported into Skyline (I’m using version 19.1) by following these two steps:

1. Make sure the .mzML spectra file you performed the search with is in the same directory as the .mzID file. If you used MetaMorpheus’s calibration, you will need to look at the Calibration Task results directory and move the calibrated .mzML spectra files in that folder to the folder with your .mzIDs, or vice versa.
2. Skyline will let you try to open files labeled “.mzID” but it will crash upon trying to open them, saying that “.mzID” is not a recognized file type. Simply rename the file extension to “.mzid” (lower-case) and it will import successfully.

I will post about issue # 2 on Skyline’s support forum when I get a chance. It might have more weight if you do it in addition to me, since you’re a user of both softwares :)

One more thing – I noticed a while ago that G-PTM-D are incredibly slow to import into Skyline. They do a re-digestion of the protein database, with every modification listed in the .mzID as a variable mod. Since GPTMD can discover so many modifications, Skyline creates many, many, many peptide permutations. I posted about this a while ago but I’m not sure they are interested in pursuing it, or have the manpower to solve it. Again, if you make a post on this issue (https://skyline.ms/announcements/home/support/thread.view?entityId=b5bce339-523b-1036-8c20-e465a393e12b&_docid=thread%3Ab5bce339-523b-1036-8c20-e465a393e12b) it may help move things forward, if importing GPTMD results into Skyline is of interest to you.

Please let me know if that helped!

One last thing – I forgot to mention that Nick Shulman mentioned in the Skyline support thread that I sent you that there is a trick you can use to import GPTMD results into Skyline:

“One thing that you can do instead is cancel out of the "Import Peptide Search" wizard once you get to the part where it's asking for the FASTA file. Then, in Skyline, use the menu item: View > Spectral Libraries and then use the "Add All" button to add the peptides from the spectral library into your document.”