1. I selected my. xtan. xml file in the importer. It correctly found my
I selected my .xtan.xml file in the importer. It correctly found my .raw file that matched. Then, I have to say what enzyme to use, so I made one up for no enzyme (all the amino acid letters|-). So, I tried adding the list of proteins that I used to search against in the .fasta box.

2. I found the file and imported my FASTA protein library.

3. Then, this message. I clicked “Remove”

4. Then, this message. I’m not sure what it means
Then, this message. I’m not sure what it means. So I click OK, then try again, this time keeping the protein list, but I still get the same message. I can’t get any farther, so I have to press “cancel” on the “Import FASTA screen”

5. Things that I noticed:
-When I opened the Spectral Library Explorer I did not get the window asking about the library modifications, like it shows in the tutorial.
-The retention time is not in minutes as expected, but in seconds
-The file association is to the .mgf file, rather than the .raw file for some reason.

6. Then, I clicked “Add all…”
Then, I clicked “Add all…”. This works: they all show up in the target panel, and I can see the peaks.
But, as you can see the matching to the chromatogram peaks is not present.

7. In library details, I see the association is with the
In library details, I see the association is with the .mgf file, not the .raw file.

8. If I look in the .mgf file, I see that the TITLE line is not pointing to the raw file, but rather a number. Is this what is wrong?
I also see that my RTINSECONDS is wrong—they are all showing ups as “1”
MASS=Monoisotopic
BEGIN IONS
TITLE=File21087 Spectrum1 scans: 4
PEPMASS=
CHARGE=1+
RTINSECONDS=1
SCANS=4
END IONS

9. So, I went back to my. raw file and remade the
So, I went back to my .raw file and remade the .mgf file with these settings in MSConvert.

10. This is the format that came out. It looks correct, except the “. 4. 4
This is the format that came out. It looks correct, except the “.4.4.1” after the file name is added by MSConvert for some reason.
Then, I repeated my search in X!Tandem with the new .mgf file.

11. After getting a new .xml result file, I opened a new skyline file and imported the new result. It successfully matched to the .raw file. Then I got this screen again. I added my protein library. I got the same error message. So, I clicked cancel.

12. The spectral library still points to the
The spectral library still points to the .mgf file instead of the raw file, and the retention time is still represented in seconds, rather than minutes.
I tried Add all again, which did add them to the target list, but, again, no chromatogram peaks.