Liberator
Overview
This application creates a library of annotated spectra generated from a pepxml file.
Usage
usage: Liberator <PepXML> [-a] [--auto-scan] [-b <arg>] [-d <arg>] [-e
<arg>] [-f <arg>] [--filter <arg>] [--force] [-g <arg>] [-h] [-i <arg>] [-l]
[--loss-advanced <arg>] [--loss-phosphate] [--loss-verbose]
[--max-loss-sites <arg>] [--max-peak-annots <arg>] [--maxCharge <arg>]
[--maxMZ <arg>] [--mgf-scan-pattern <arg>] [--minCharge <arg>] [--minMZ
<arg>] [--msLevel <arg>] [-n] [--no-merge] [-o <arg>] [-p <arg>] [-q] [-r <arg>] [--tol]
[-v]
-a,--average set the average mass mode for peptide mass
calculation
by default: monoisotopic.
--auto-scan enable auto scan number (from scan 1 to n).
-b,--bSize <arg> batch size for MS files
by default: 10000.
-d,--dir <arg> define the resource directory(ies) ('path1, ..., pathn') from where
MS data files will be recursively searched. The basename file is defined in
each "spectrum" attribute of '<spectrum_query>' tag with the following format
('basename.start_scan.end_scan.charge')
by default: empty path (a unique MS resource file path is defined for each
'<msms_run_summary>' as defined in http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_vXYZ.xsd).
-e,--ext <arg> extension for MS2 spectrum files
by default: mgf.
-f,--frags <arg> define the fragmentation type(s):
a,b,c,x,y,z for backbone type fragments
i for immonium and p for precursor
by default: b,y.
--filter <arg> set the filter for peptide to spectrum search hit selection.
The expression operands are defined from search_score 'name' and
analysis_result 'analysis' pepxml attribute value (ex:
(peptideprophet ≥ 0.9) & (hyperscore > 400))
by default: peptideprophet ≥ 0.9.
--force force the conversion of already converted
MS files (MS data files serialized in /tmp).
-g,--graph <arg> export PSM graph file.
-h,--help print this message.
-i,--setting-file <arg> give a property file with all input
settings.
-l,--loss enable neutral loss fragmentation.
--loss-advanced <arg> enable the user to define losses himself.
Set the amino-acid target and the kind of loss action based on the grammar
below:
// Examples of Rules
# simple:
C -> -16
# AA class target:
[KNQR] -> -23.5
# AA class with a modif range as target:
[KNQR]/40:80 -> del
# alternative editions:
[KNQR]/40:80 -> -23.5, del
# few rules:
[KNQR]/40:80 -> -23.5, del ; C -> -16
# sequential edit actions:
Y/79.9:80.1 -> del-18 ;
// Grammar Definition
rules: rule (';' rule )*;
rule: target '->' actions;
target: aaclass ('/' range) ?;
actions: action (',' action)*;
action: (modaction)+ | remaction (modaction)*;
modaction: '-'
INT | '-' FLOAT;
remaction: 'del';
aaclass: AA | '[' AA (AA)* ']';
range: number ':' number;
number: INT | FLOAT;
// Lexers
INT: '0'..'9'+ ;
FLOAT: INT ('.' INT);
AA: 'A'..'Z' ;
--loss-phosphate enable phosphate loss on phosphated [YST]
amino acid fragments.
by default: false.
--loss-verbose enable loss rule verbosity mode.
by default: false.
--max-loss-sites <arg> limit the maximum of loss sites
by default: 2
--max-peak-annots <arg> limit the maximum of annotations displayed
by peak
by default: no limit
--maxCharge <arg> maximal precursor charge
by default: 10.
--maxMZ <arg> maximal precursor mz value
by default: 5000.0.
--mgf-scan-pattern <arg> set the pattern to extract scan number from
mgf TITLE tag
--minCharge <arg> minimal precursor charge
by default: 1.
--minMZ <arg> minimal precursor mz value
by default: 100.0.
--msLevel <arg> level of ms spectra
by default: 2.
-n,--no-clobber do not overwrite existing converted MS
files (MS data files serialized in /tmp).
--no-merge disable the merging of MS spectra matching
the same peptide/z.
-o,--output <arg> set the output filename
-p,--precision <arg> define the number of fractional digits for
output
by default: 4.
-q,--quiet quiet mode (verbose off)
by default: false.
-r,--priority-rule <arg> set the annot precedence rule for
multi-annotated peaks:
// Grammar Definition
rules: rule ('>>' rule )*;
rule: rule-ion | rule-num
rule-ion: 'ion' : type-seq
rule-num: 'loss'|'charge'|'mzdiff':(ascent|descent)?
type-seq:
ion-type ('>' ion-type)+
ion-type: 'a' | 'b' | 'c' | 'x' | 'y' | 'z'
by default: charge>>ion:y>b>>loss>>mzdiff.
--tol define the tolerance for mz fragment peak
comparison
by default: 0.1.
-v,--version print the version info.
Releases
The latest version v1.47 -
Download app with
the default properties file.
Rel1.47
| Type | Summary |
| Bug fixed | Serialized MS data was corrupted when scan number
was exceeded 99999 (scan number limit is now of 1016-1). |
Rel1.46
| Type | Summary |
| New | Param --no-clobber prevent the default overwrite of existing
converted MS files. |
| New | Param --no-merge prevent the merge of MS spectra that match
the same peptide/z. |
Rel1.44
| Type | Summary |
| Change | Liberator interrupted the library spectra process
while building an ambiguous peptide. Such a peptide contains
ambiguous or undefined amino-acid(s), preventing the computation of
correct fragmentation spectrum. It now just warns the user. |
Rel1.43
| Type | Summary |
| Change | Param --dir now supports many directory resources
like in "dir1, dir2". |
| Bug fixed | In release 1.42, annotated spectra were hugely
duplicated in the created library. |
Rel1.42
| Type | Summary |
| New | New parameter --force to force the reconversion
of MS data files. |
| Bug fixed | MGF reader bug: a spectrum builder exception was
thrown while reading some MGF files with multiple retention times. |
Rel1.41
| Type | Summary |
| New | New parameter --auto-scan auto increment
scan numbers for MS data. |
| New | New parameter --mgf-scan-pattern <arg>
set the regular expression to extract scan number from TITLE tag (mgf format only). |
Rel1.4
| Type | Summary |
| New | New parameter --max-peak-annots <arg>
limiting the maximum number of annotations by peak. |
| Change | Change the grammar of parameter --priority-rule. |
Rel1.3
| Type | Summary |
| Bug fixed | Some problematic MGF entries with overlaps
between "SCANS" leading to crash while reading the pepxml. |
Rel1.2
| Type | Summary |
| New | New parameter --max-loss-sites <arg>
limiting the maximum number of simultaneous loss by fragment. |
| New | Enable progress bar for MSn processing. |
| New | New parameter --loss-verbose enabling
verbose mode for loss rule specifications. |
Rel1.1
| Type | Summary |
| New | New parameter --loss-phosphate. |
Rel1.0
| Type | Summary |
| New | New parameter --loss-advanced. |
Rel0.6
| Type | Summary |
| Runtime | Task name in progress bar (left margin) |
| Bug fixed | mixed-mode: merge msms_run_summary(s) in one
(no more peptide redundancies) |
Rel0.5
| Type | Summary |
| Runtime | Support multi-resources MS data.
The file basename is coded in the attribute 'spectrum'
of the pepxml element 'spectrum_query'. |
Rel0.2
| Type | Summary |
| Change | Change the --pp-threshold <numeric> with --filter <inequation expression>. |
