dockerprotim/peptimapper repository overview

run PepNovo_bin with default options : -model CID_IT_TRYP and -PTMs C+57:M+16 and convert output format to be compatible with PMMatch.
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# usage: LXRunPepNovo [-v] [-h] [-t taglen] [-n numsol] mgf_or_pkl_files+
# usage: -v : verbose
# usage: -h : print this help and exit
# usage: -t : set tag length (default 3) (only lengths 3-6 are allowed)
# usage: -n : set max number of solutions (default 10)

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PepNovo_bin output file : 

# Tags generated by PepNovo+
SpectrumTITLE.PSTId NTermMass CTermMass Tag ParentMass Score
...
%EndOfTags
...repeat foreach tag

with : 
	Spectrum TITLE : MGF file spectrum "TITLE=" value
	PSTId : spectrumId '.' pstIndex
		where pstIndex goes from 1 to number of PSTs generated for this spectrum
	NTermMass : mass of the NTerm part of the PST
	CTermMass : mass of the CTerm part of the PST
	Tag : PST Tag
	ParentMass : mass of the Parent Ion (M+H)
	Score : PST score

LXRunPepMatch run successively 3 scripts PMtrans, PMMatch, and PMClust :
- PMTrans : will translate a DNA file (fasta format) into six-frame translations for further use by PMMatch
- PMMatch : match PSTs found by LXRunPepNovo on the six-frame translation of DNA sequence(s). A hit correspond to the location of a PST on a translated sequence.
	with following default options : -n 1 (maximum number of modified residues), -m 0 (maximum number of miscleavage(s)), -a /EctoLine/scripts/data/aa_mono.ref (aminoacid reference file), -e /EctoLine/scripts/data/trypsine.ref (digestion enzyme reference file)
- PMClust : clusterizes hits into clusters and projects hits position back to the original (untranslated) DNA sequence.

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# usage: LXRunPepMatch [-v] [-h] [-f] [-F] [-D tolerance] [-t minhit] [-T minpep] [-d dist] chromo_fasta tag_file+
# usage: -v : verbose
# usage: -h : print this help and exit
# usage: -f : force recompute chromosome translation
# usage: -F : force recompute PMMatch
# usage: -D : set mass tolerance (default 0.5)
# usage: -t : set min number of hit per cluster (default 3)
# usage: -T : set min number of peptide per cluster (default 2)
# usage: -d : set clustering distance (default 5000)


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LXRunPepMatch output files : 

>>> hit file :

SequenceName D|R frame SeqLength [Sequence Comment]
PST_output_line_from_PepNovo_bin 
F|N|C posMn posMc posTn posTc pepSeq pepMatch nbMis nbOver mbMod score
%EndOfHits
...repeat foreach hit

SequenceName : name of DNA sequence (from fasta file)
D|R : D for direct strand R for reverse strand
frame : translation frame (1, 2 or 3)
SeqLength : length of original DNA sequence

PST_output_line_from_PepNovo_bin : PST line from PepNovo_bin 
PSTId NTermMass CTermMass Tag ParentMass Score
(see PepNovo_bin output format)

F|N|C  :  Type of hit 
F : Full hit : both N and C term masses match
N : N_Partial hit : C term mass is missing
C : C_Partial hit : N term mass is missing

posMn : position of the N term part of PST on the proteic sequence (see figure)
posMc : position of the C term part of PST on the proteic sequence (see figure)
posTn : start position of the tag part of PST on the proteic sequence (see figure)
posTc : end position of the tag part of PST on the proteic sequence (see figure)

   (Mn)---------[  tag  ]----------(Mc) 
   |            |       |              |
   |            |       |              |
___|____________|_______|______________|_________
   posMn       posTn   posTc      posMc
   
   Note: all positions are given on the translated sequence
   Note: for partial hits (N or C types), the missing posMx position is indicated by 0
 
 pepSeq : the matched peptide as it appears on the translated sequence.
 	Note: pepSeq is flanked by the preceeding and following symbol on the sequence :
 		<preceding>.peptide.<following>

	special flanking symbols are '*' for sequence extremities and 'X' for a stop codon

 pepMatch : the matched peptide as matched by PMMatch, i.e. with possible modifications. if present modified amino-acids are indicated by lowercase characters. Moreover the tag part of the PST is indicated between brackets.

 nbMis, nbOver : number of mis- and over-cleavages. Normally, a hit should be flanked by two enzyme cut sites or a stop codon on the Cterm or a Met on a N-Term and no cut sites should appear within the peptide.
	An extra cut site within the peptide is called a miscleavage.
	A missing cut site at any extremity is called an overcleavage

	Note: the maximum number of mis- and over-cleavage can be set by the -m and -M options
	Note: a stop codon at the C-term part is not counted as an overcleavage
	Note: a Methionine at the N-term part is not counted as an overcleavage unless the -y option is set to 0.

 nbMod :  number of modified aa in the peptide.

	Note: allowed modifications are indicated in the 'aa_mono.ref' runtime configuration file (see below).
	Note: the maximum number of modified aa can be set with the -n option
	Note: in the current version, no modifications are allowed in the tag part of the PST, only modifications in the N or C terminal masses are taken into account.

 score: PST score. In the current version this is simply the PST score. This will be changed in the future.
 
>>> clust file :

CLUSTER idCluster nbHits nbFullHits nbPepHits score
SequenceName 'D|R' frame SeqLength [Sequence Comment]
// the two following lines are rpeated for each hit in the cluster
PST_output_line_from_PepNovo_bin 
HIT_output_line_from_PMMatch 
%EndOfCluster
...repeat foreach cluster

with :

idCluster  : an integer starting at 1 
nbHits     : total number of hits (full + partials)
nbFullHits : number of full hits
nbPepHits  : number of different peptides
score      : score of cluster (in the current version the sum of full hits scores)

SequenceName : name of DNA sequence (from fasta file)
D|R : D for direct strand R for reverse strand
frame : translation frame (1, 2 or 3)
SeqLength : length of original DNA sequence
	Note: this line is identical to the sequence line in the hit output of PMMatch
	!!! Important note: the posMn, posMc, posTn, posTc positions are now given as nucleotide positions on the original DNA sequence.

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#usage: LXQualify [-v] [-h] [-f] cluster_file gff_directory
#usage: -v : verbose
#usage: -h : print this help and exit
#usage: -f : force recompute chromosome translation

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# usage: LXClust2Gff [-v] [-h] gff_directory output_directory cluster_file+
# usage: -v : verbose
# usage: -h : print this help and exit