MSGF new enzyme help

[BaylorSci]

Although the enzyme support for MSGF is really good, i have recently starting digesting my samples in a combination of Lys-C/Trypsin (specifically https://www.promega.com/products/mass-spectrometry/proteases-and-surfactants/trypsin_lys_c-mix_-mass-spec-grade/?catNum=V5071), which is not currently supported in the documentation (combination of enzymes).

What i would like to do is create a new enzyme param to account for this. However, i have never done this before and wonder whether anybody could help? From my limited understanding it would likely be a combination of 1 and 3

Tryp,KR,C,Trypsin # 1

LysC,K,C,Lys-C # 3

Proprosed LysC/Tryp,**X,X,**Lys-C/Tryp # 10: Combination Lys-C/Tryp However, i'm unsure where to find the information for the CleaveAt site or the terminus. Any help with this would be very much appreciated!!!!

[alchemistmatt]

Trypsin cleaves after K or R while LysC only cleaves after K. For your samples, just use Trypsin as your enzyme, optionally doing a partially tryptic search. For example, in a parameter file (specified with -conf) you'd use

#Enzyme ID
#  0 means No enzyme used
#  1 means Trypsin (Default); use this along with NTT=0 for a no-enzyme search of a tryptically digested sample
#  2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: Glu-C, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: No Enzyme (for peptidomics)
EnzymeID=1

#Number of tolerable termini
#  The number of peptide termini that must have been cleaved by the enzyme (default 1)
#  For trypsin, 2 means fully tryptic only, 1 means partially tryptic, and 0 means no-enzyme search
NTT=1

e.g. MSGFPlus_PartTryp_MetOx_20ppmParTol.txt at https://github.com/MSGFPlus/msgfplus/tree/master/docs/ParameterFiles

Or, if using command line arguments, use

-e 1 -ntt 1