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Rappsilber-Laboratory / XiSearch

XiSearch
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setting xiSEARCH (DSSO) #62

Closed 13651809703 closed 1 year ago

13651809703 commented 2 years ago

Dear xiSEARCH group,

I am a fresh user of xiSEARCH. Thanks so much for your powerful tool for my CLMS work. Would you kindly help me set xiSEARCH parameters?

1) No amidated and hydrolyzed DSSO were found in variable modifications settings. (version 1.1.6.7). I saw these parameters for BS3.

2) the difference of DSSO(large scale) and DSSO(small scale). For whole proteome-wide, is it right to use DSSO (large scale) to reduce search time?

Thanks a lot. I am looking forward to your reply.

lutzfischer commented 2 years ago

DSSO large scale and small scale come with modifications defined as part of the crosslinker.

They are defined in the BasicConfigEntries.conf file DSSO(Large Scale)=crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:DSSO;MASS:158.0037648;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);LINEARMODIFICATIONS:NH2,17.026549105,OH,18.0105647,loop,0;STUBS:A,54.0105647,S,103.9932001,T,85.9826354

DSSO(Small Scale)=crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:DSSO;MASS:158.0037648;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);MODIFICATIONS:NH2,17.026549105,OH,18.0105647,loop,0;STUBS:A,54.0105647,S,103.9932001,T,85.9826354

The part that defines the modifications is LINEARMODIFICATIONS:NH2,17.026549105,OH,18.0105647,loop,0 and MODIFICATIONS:NH2,17.026549105,OH,18.0105647,loop,0 respectively. Difference being that with peptides containing the as LINEARMODIFICATIONS defined modifications will only be considered as part of linear peptides, while when they are defined as MODIFICATIONS these peptides can also be part of a crosslink.

In both cases the modification mass is the added mass to the crosslinker. E.g. the final dssonh2 modifictaion will have a deltamass of 158.0037648Da + 17.026549105Da = 175.030313905Da.

You can also define the modifications independent of the crosslinker, in the modification section in the BasicConfigEntries.conf file. DSSO Amidated=modification:[MODE]::SYMBOLEXT:dssonh2;MODIFIED:K,S,T,Y;DELTAMASS:175.030313905 then you can define them as variable or linear in the interface. but then you should change the definition of the crosslinker to not include the modifications.

if you define them independently you could even define that e.g. only the DSSO Amidated(K) is variable while the other are only considered for linear peptide. DSSO Amidated(K)=modification:[MODE]::SYMBOLEXT:dssonh2;MODIFIED:K;DELTAMASS:175.030313905 DSSO Amidated(S)=modification:[MODE]::SYMBOLEXT:dssonh2;MODIFIED:S;DELTAMASS:175.030313905 DSSO Amidated(T)=modification:[MODE]::SYMBOLEXT:dssonh2;MODIFIED:T;DELTAMASS:175.030313905 DSSO Amidated(Y)=modification:[MODE]::SYMBOLEXT:dssonh2;MODIFIED:Y;DELTAMASS:175.030313905

the same applies for the other modifications.