NIST library with Unimod, but untypical modifications

support
NIST library with Unimod, but untypical modifications solis  2020-11-26
 

Dear Skyline team,

thanks for your continuous improvement of the software and the tools within it.

I have an issue with Skyline recognizing "Propionyl" modifications in a NIST library as well as Methy and Propionyl modifications co-occurring on the same site. As you may know, these PTMs are relevant in the context of some protocols for histone PTM analyses. Could you please let me know if indeed this is a current limitation of Skyline or if something is wrong with my attached NIST library instead?

And if the former is the issue, you could then maybe make Skyline able to recognize any modification as long as its name is in the Skyline Modifications list.

Thank you very much and my best regards.

Victor Solis

 
 
Nick Shulman responded:  2020-11-26
When Skyline is reading a NIST library, this is the list of modifications that Skyline understands:

Oxidation
ICAT_light
ICAT-C
ICAT_heavy
ICAT-C:13C(9)
AB_old_ICATd0
ICAT-D
AB_old_ICATd8
ICAT-D:2H(8)
Carbamidomethyl
Carboxymethyl
Propionamide
Propionamide:2H(3)
Propionamide:13C(3)
Acetyl
Deamidation
Deamidated
Pyro-cmC
Pyro-carbamidomethyl
Pyro-glu
Gln->pyro-Glu
Pyro_glu
Glu->pyro-Glu
Amide
Amidated
Phospho
Methyl
Carbamyl
iTRAQ4plex
PEO-Iodoacetyl-LC-Biotin
Label:13C(6)
Label:13C(6)15N(1)
Label:13C(6)15N(2)
Label:13C(6)15N(3)
Label:13C(6)15N(4)
Methylthio
Leucyl
Leucyl:13C(6)15N(1)
Nitro
Dimethyl
Trimethyl
Bromo
SUMO_1
SUMO_2_3_Tryp
Smt3_R93A_Tryp
Smt3_R93A_LysC
NEDD8_LysC
Rub1_LysC
Ub_LysC
GlyGly

We have not added anything to that list since 2011, so either that is a complete list of everything one could expect to find inside of NIST library, or there is some other workaround. (I do not know which is the answer)

Where did you get this .msp file? Is there any way that you could have gotten a BiblioSpec (.blib) file instead? In a BiblioSpec library, the modifications are only described by masses, and Skyline can wait until you are using the library in a Skyline document before trying to determine the exact identity of the modification.

Someone else on the Skyline support board will probably be able to give you a better answer about what to do about this.
-- Nick
 
solis responded:  2020-11-27
Hello Nick,

thanks for the reply. Our msp library is in-house created. Unfortunately, we cannot create a blib file using Skyline due to the fact that our original text format is not in the list of formats accepted by Skyline or can be converted into them (not even ssl with its required fields).

Thus, it would indeed be great if you can extend that default list that skyline understands in a NIST library. Do you think this is feasible in a future Skyline-daily version? Given that NIST is, to some extent, compatible with Unimod names, at least a subset of nowadays "common" Unimod modifications can be added to your list (if I can suggest). For example, modifications associated with histones, because the epigenetics field/knowledge is growing.

Thank you once again and I hope somebody else from your colleagues can comment on this ticket.

Best regards =)