Closed grandrea closed 1 year ago
When there are modifications that can't be recognized by DIA-NN, you need to specify it using the --var-mod
flag: https://github.com/vdemichev/DiaNN#command-line-reference, although I am not sure why you still got the error with the --strip-unknown-mods
. This flag is suppose to let DIA-NN ignore any "unknown modifications".
Best,
Fengchao
Thanks for the help!
just to confirm- I run dia-nn with the flags
--var-mod custom1,82.0418,KSTY --var-mod custom2:100.0524,KSTY --var-mod custom3,295.0362,KSTY --var-mod custom4,202.107934,KSTY --var-mods 3
and there is a mismatch between mod masses in the log
Modification custom1 with mass delta 82.0418 at KSTY will be considered as variable WARNING: no amino acids to be modified, modification ignored Modification custom2 with mass delta 295.036 at KSTY will be considered as variable Modification custom3 with mass delta 202.108 at KSTY will be considered as variable Maximum number of variable modifications set to 3 DIA-NN will optimise the mass accuracy automatically using the first run in the experiment. This is useful primarily for quick initial analyses, when it is not yet known which mass accuracy setting works best for a particular acquisition scheme. Cannot find a UniMod modification match for custom1: 2.07547 minimal mass discrepancy; using the original modificaiton name Cannot find a UniMod modification match for custom2: 46.0068 minimal mass discrepancy; using the original modificaiton name Cannot find a UniMod modification match for custom3: 138.935 minimal mass discrepancy; using the original modificaiton name
This seems fixed when I add
--original-mods
as a flag. I suppose that's ok?
Yes, --original-mods
will also solver your problem in another way: --original-mods disables the automatic conversion of known modifications to the UniMod format names
There is also a --mod
flag which seems related: --mod [name],[mass],[optional: 'label'] declares a modification name. Examples: "--mod UniMod:5,43.005814", "--mod SILAC-Lys8,8.014199,label"
.
To be honest, I always can't distinguish those three flags....
Best,
Fengchao
Hello,
I am trying to run the DDA/DIA worfflow "DIA_SpecLib_Quant" on fragpipe 20.0 I am searching both dda and a dia files, passing on the spectral library built from the dda runsto dia-nn. I define some custom modifications present in my sample in the dda side. The DDA search completes, but then dia-nn to crashes with "unknown modification". I see in the log that dia-nn gets launched with "strip unknown mods"... is this the reason? any idea on how to do dda, library generation and dia with custom mods? I do not need to replace library spectra with predicted.
Many thanks in advance!