vdemichev
commented
5 months ago The first-pass report is non-empty in this case, but no biotinylated peptides are identified - it's very likely that none are detectable. One important point: need to add --no-cut-after-mod Biotin. The MBR (second pass) report is empty because nothing passed the global q-value filter.
General comments:
- Worth trying with max variable mods set to 2 and without M(ox) during predicted library generation
- Deep learning prediction was enabled, which is unnecessary, since a predicted library was loaded
- Better to fix mass accuracies and the scan window
Sree702
Hi @vdemichev,
I am a new user of DIA-NN and was trying to perform search with Biotin modification. I created a spectral library from fasta database using --strip-unknown-mods in the additional commands I then used this spectral library for my raw file searches by using "--var-mod Biotin,226.077598,nK and --monitor-mod Biotin". However, the searches identified no peptides or proteins and the report files were empty. I am not sure as to where am I going wrong. Could you please help me identify the problem? In the log file, I did notice this line "Cannot find a UniMod modification match for Biotin: 69.9765 minimal mass discrepancy; using the original modification name". So, I tried providing the name as Unimod #3 which is the modification in the unimod database but with no use. Combined_logs_biotin_searches.txt I have enclosed a copy of the search logs for your reference.
I would greatly appreciate the help with troubleshooting this issue. Thanks in advance for the help