Peptide library building from MaxQuant.

Peptide library building from MaxQuant. luzjpaulo  2019-05-20

I created a library from MaxQuant using the latest Skyline-daily update but I found out an issue. Skyline-daily gives me very bad peptide spectrum matches while Skyline does not have this problem.

matt.chambers42 responded:  2019-05-21

Hi Paulo,

Can you attach the FASTA as well? I'm trying to reproduce the issue.

luzjpaulo responded:  2019-05-22
matt.chambers42 responded:  2019-05-24

Unfortunately I'm not able to reproduce. Where are you seeing the "very bad peptide spectrum matches"? When I look at the spectral libraries created by 4.2 and daily I see the same number of peptides, but the mods are correct in the daily version because of the MaxQuant fixed terminal mods bugfix.

luzjpaulo responded:  2019-05-24

Hello Matt,

Thank you for the attention. I guess it might be some bug in my PC. I tried to create some libraries with different cut off scores and I got some strange results. When I used the cut off score equal to 1, for instance, I got 7 peptides that are not the best ones. while I tried using the cut off scores of 0 and 0.95 I got the same number of peptides. Do you have any thoughts on that? I am not a specialist so I might missing something.

matt.chambers42 responded:  2019-05-28

Where are you getting the 7 peptide number from? A cutoff of 1 should mean all spectra are allowed (minus duplicates and ambiguous).

luzjpaulo responded:  2019-05-29

I found the number 7 in the spectral library explorer. I found a solution to my problem though . I put the msms, mqpar and modificatios files in a different folder and I built the library using the embebbed option. At this time the library showed very good matches. I think my problem is solved.