Dig2MZ

This application digests fasta proteins and reports all peak's mz, charge and other infos.

usage: Dig2MZ <fasta> [-a] [--cyscam] [-d <arg>] [-e <arg>] [-f <arg>] [-h] [-i <arg>]
	[-L <arg>] [-l <arg>] [-m <arg>] [--non-verbose] [-o <arg>] [-p <arg>] [-q <arg>]
	[-u <arg>] [-v]
 -a,--average                     set the average mass mode for peptide mass
                                  calculation
                                  by default: MONOISOTOPIC.
    --cyscam                      modification of all protein's cysteins
                                  by S-carboxamidomethyl cysteines (CysCAM, +57 Da).
 -d,--delimiter <arg>             define the field delimiter to display
                                  by default: \t.
 -e,--enzymes <arg>               define enzymes that digest proteins separately with:
                                  enzyme name among 'Caspase-1, Caspase-10, Glu-C_bicarbonate, Caspase-3,
                                  Thermolysine, Lys-C, Pepsin_pH1.3, Caspase-8, Glu-C_phosphate, Caspase-9,
                                  Caspase-5, CNBr, ChymoTrypsin_lowspec, Trypsin, ChymoTrypsin_FYL,
                                  Proteinase-K, Caspase-7, Pepsin_pHgt2, ChymoTrypsin_highspec,
                                  BNPS-Skatole, Enterokinase, Caspase-6, Arg-C, Asp-N, ChymoTrypsin_FYLW,
                                  Caspase-4, Caspase-2'.
                                  or custom motifs respecting the following grammar:
                                  <pre-cut> <cut-token> <post-cut>
                                  <cut-token> := '|'
                                  <pre-cut> := (<AA> or <AA-class>)+
                                  <post-cut> := (<AA> or <AA-class>)+
                                  <AA> := [A-Z]
                                  <AA-class> := '[' AA+ ']'
                                  by default: Trypsin.
 -f,--fields <arg>                define the fields to display (1:MZ, 2:Charge,
                                  3:Enzyme, 4:Seq, 5:MC)
                                  by default: [1, 2, 3, 4, 5].
 -h,--help                        print this message.
 -i,--setting-file <arg>          give a property file with all input settings.
 -L,--pept-len-filter <arg>       define a filter over length of digested peptides
                                  by default: 6.
 -l,--pept-mz-lower-filter <arg>  define the lower mz bound (included) of
                                  digested peptides
                                  by default: 400.
 -m,--mc-max-num <arg>            define the number of maximum missed cleavages
                                  (for digestion)
                                  by default: 1.
    --non-verbose                 non verbose mode (no header for settings).
 -o,--oximet-max-num <arg>        define the number of maximum oxidated
                                  methionines
                                  by default: 0.
 -p,--precision <arg>             define the decimal precision for any
                                  mass-to-charge ratio
                                  by default: 6.
 -q,--pept-charge-filter <arg>    define a filter over charges on digested
                                  peptides as a sequence of integers and/or intervals like in 1, 2, 3:5,
                                  10:7
                                  by default: [2, 3].
 -u,--pept-mz-upper-filter <arg>  define the upper mz bound (included) of
                                  digested peptides
                                  by default: 2000.
 -v,--version                     print the version info.

      

# a first way to execute the application with lots of options
# the results are redirected in file digests.out and errors in digests.log
$ java -jar Dig2MZ-1.1.jar -a -e Lys-C -f 1,2,4,5 -l 1 -p4 -q 2:4 uniprot-human.fasta > digests.out 2> digests.log

# .. or the more compact way with all options defined in a setting file
$ java -jar Dig2MZ-1.1.jar -i settings.properties uniprot-human.fasta > digests.out 2> digests.log

$ more digests.out
# ==================================================================
# Generated by Dig2MZ v.1.1
#
# Input Proteins ---------------------------------------------------
#	read from file                 uniprot-human_swissprot.fasta
#	modified (fixed) with          CYS_CAM
#	digested by enzyme             [Lys-C, pattern: K|X, mc#=1]
# Digested Peptides ------------------------------------------------
#	filtered with charges          [2, 3, 4]
#	filtered with length           >= 1
#	filtered over mzs in interval  [400.0, 2000.0]
#	with masses computed in mode   AVERAGE
# Output Fields ----------------------------------------------------
#	all                            [MZ, Charge, Enzyme, Seq, MC]
#	selected indices               [1, 2, 4, 5]
# Real
#	Decimal precision format       4
# ==================================================================
MZ	Charge	Seq	MC
1192.3452	3	NDDNAITSPIAGKTSVLRAIPVEVLANSYDISTK	1
894.5108	4	NDDNAITSPIAGKTSVLRAIPVEVLANSYDISTK	1
1355.1842	2	LILSFSLC(C2H3NO)LMVLSC(C2H3NO)SAQLLPWQK	0
658.7105	2	NDDNAITSPIAGK	0
1578.9621	2	MSTKLILSFSLC(C2H3NO)LMVLSC(C2H3NO)SAQLLPWQK	1
1052.9772	3	MSTKLILSFSLC(C2H3NO)LMVLSC(C2H3NO)SAQLLPWQK	1
694.2949	2	AGREGLEWVELK	0
463.1991	3	AGREGLEWVELK	0
651.3932	3	RGGSGRSNGLEQAFC(C2H3NO)NLK	0
488.7968	4	RGGSGRSNGLEQAFC(C2H3NO)NLK	0
556.3634	4	NGRQEVEVFRPFQSRDEK	0
518.5931	2	ERERFSIV	0
895.6627	3	AGREGLEWVELKNDDNAITSPIAGK	1
671.9989	4	AGREGLEWVELKNDDNAITSPIAGK	1
1139.3187	2	TSVLRAIPVEVLANSYDISTK	0
...

# get digested peaks and sort by mz
$ tail -n+19 digests.out | sort -k1 -n | uniq > digests_sorted.out

$ more digests_sorted.out
MZ	Charge	Seq	MC
400.0003	4	ILLEGRRLISDALK	0
400.0006	5	HMEDPLEMERSPQLRK	0
400.0032	4	TAIQQLRSVIRALK	0
400.0057	5	IRQFEEQFERERNSK	0
400.0065	5	AFVYNSSLVSHQEIHHK	0
400.0080	5	RDATHDYRQALATHVNK	0
400.0101	5	ELVERRRTMMEDFRK	0
400.0101	5	PMVNHAEASRLNIERMK	0
400.0117	5	NSPRLRMRTETPSHWK	0
400.0124	5	PQLHSMVARSLC(C2H3NO)RNAAGK	0
400.0138	5	LC(C2H3NO)RLSMQC(C2H3NO)LRDFRIK	0
400.0145	5	HVIIGFSIENSHDRIMK	0
400.0152	5	RLMADELERFTSMRIK	0
400.0161	5	RVTRTGFEDGLFAGWRK	0
400.0167	5	VEQLFGLGLRPRGEC(C2H3NO)HK	0
400.0210	5	DHLTLGTGVAGIDMRRGVK	0
400.0212	5	RAALC(C2H3NO)FRRNLGTYNRK	0
400.0233	5	SIQISHFNPPPPHLRQK	0
400.0240	5	FYASVRC(C2H3NO)DIRRIQALK	0
...
      

The latest version is v1.21 - Download app and the default properties file.

Rel1.21

Rel1.1