mods.txt for TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8, and Label Free

[rkimoakbioinformatics]

Describe the question or problem I made mods.txt files for TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8, and Label Free experiments. Can anyone check the files and let me know if they are properly made?

Details mods_tmt6.txt

NumMods=3
C2H3N1O1,C,fix,any,Carbamidomethyl
O1,M,opt,any,Oxidation
H-1N-1O1,NQ,opt,any,Deamidated
229.1629,*,fix,N-term,TMT6plex
229.1629,K,fix,any,TMT6plex

mods_tmt10.txt

NumMods=3
C2H3N1O1,C,fix,any,Carbamidomethyl
O1,M,opt,any,Oxidation
H-1N-1O1,NQ,opt,any,Deamidated
229.1629,*,fix,N-term,TMT10plex
229.1629,K,fix,any,TMT10plex

mods_tmt11.txt

NumMods=3
C2H3N1O1,C,fix,any,Carbamidomethyl
O1,M,opt,any,Oxidation
H-1N-1O1,NQ,opt,any,Deamidated
229.1629,*,fix,N-term,TMT11plex
229.1629,K,fix,any,TMT11plex

mods_itraq4.txt

NumMods=3
C2H3N1O1,C,fix,any,Carbamidomethyl
O1,M,opt,any,Oxidation
H-1N-1O1,NQ,opt,any,Deamidated
144.102063,*,fix,N-term,iTRAQ4plex
144.102063,K,fix,any,iTRAQ4plex

mods_itraq8.txt

NumMods=3
C2H3N1O1,C,fix,any,Carbamidomethyl
O1,M,opt,any,Oxidation
H-1N-1O1,NQ,opt,any,Deamidated
144.102063,*,fix,N-term,iTRAQ8plex
144.102063,K,fix,any,iTRAQ8plex

mods_label_free.txt

NumMods=3
C2H3N1O1,C,fix,any,Carbamidomethyl
O1,M,opt,any,Oxidation
H-1N-1O1,NQ,opt,any,Deamidated
H-2O-1,E,opt,N-term,Pyro_glu
H-3N-1,Q,opt,N-term,Pyro-glu

[alchemistmatt]

Go to http://www.unimod.org then click "Login as Guest". Now search for TMT to learn the official names of the TMT mods. Repeat for iTRAQ. You'll find:

Name	Mass	Notes
TMT6plex	229.162932	Use this mod mass and mod name for TMT6, TMT10, and TMT11
TMTpro	304.207146	Use for 16-plex TMT
iTRAQ4plex	144.102063	4-plex iTRAQ
iTRAQ8plex	304.205360	8-plex iTRAQ
Glu->pyro-Glu	-18.010565	Empirical formula: H(-2) O(-1)
Gln->pyro-Glu	-17.026549	Empirical formula: H(-3) N(-1)

The web page also has the empirical formulas, e.g. H(12) C(4) 13C(3) N 15N O. Both the iTRAQ mods and the TMT mods have 13C and 15N, which MS-GF+ does not support. That is why you had to use the monoisotopic mass, instead of the empirical formula.

Examining what you provided, you need to change from TMT10plex to TMT6plex and from TMT11plex to TMT6plex. Also, your mod mass for 8-plex iTRAQ is incorrect: we use 304.205360 (which is very close to the listed values of 304.205360 and 304.199040). You should also switch from interim names Pyro-glu and Pyro_glu to the final names: Gln->pyro-Glu and Glu->pyro-Glu

I would also advise you to run MS-GF+ using parameter files instead of with these mod files. For more info, see the MS-GF+ Documentation, specifically https://msgfplus.github.io/msgfplus/MSGFPlus.html

The help pages also include a link to example parameter files, including both TMT and iTRAQ, though our examples don't include the deamidation that you have. Including that shouldn't hurt anything. Examples:

• https://github.com/MSGFPlus/msgfplus/blob/master/docs/ParameterFiles/MSGFPlus_Tryp_DynMetOx_Stat_CysAlk_TMT_6Plex_20ppmParTol.txt
• https://github.com/MSGFPlus/msgfplus/blob/master/docs/ParameterFiles/MSGFPlus_PartTryp_DynMetOx_Stat_CysAlk_iTRAQ_8Plex_20ppmParTol.txt

[rkimoakbioinformatics]

@alchemistmatt Thank you so much. I am new to MS-GF+ and MS analysis software, so your answer helped me so much!