Fasta2MS

This application digests and fragments fasta proteins into annotated MS spectra.

MS/MS spectra are returned in the standard output in mgf format.

usage: Fas2MS <fasta> [-a] [-d <arg>] [-f <arg>] [-h] [--no-digestion]
	[-p <arg>] [-q <arg>] [-v]
 -a,--annot-mode             enable peak annot mode.
 -d,--digest-motif <arg>     define the motif for digestion:
                             <pre-cut> <cut-token> <post-cut>
                             <pre-cut> := (<AA> | <AA-class>)+
                             <post-cut> := (<AA> | <AA-class>)+
                             <AA> := [A-Z]
                             <AA-class> := '[' AA+ ']'
                             by default: Trypsin, [KR]|[^P].
 -f,--frag-types <arg>       define the fragment type(s):
                             a,b,c,x,y,z for backbone type fragments
                             i for immonium and p for precursor
                             by default: b,y.
 -h,--help                   print this message.
    --no-dig                 non digestion mode.
 -p,--precision <arg>        define the decimal precision for any
                             mass-to-charge ratio
                             by default: 6.
 -q,--charge-numbers <arg>   define the list of charge for fragments:
                             a sequence of integers like in 1,2,3:5,10:7
                             by default: 1.
 -v,--version                print the version info.

      

The latest version is v1.2 - Download app with java sources.

Rel1.2

Rel1.1

Rel1.0