/usr/tpp_install/tpp/bin/xinteract
/usr/tpp_install/tpp/bin/xinteract (TPP v5.0.0 Typhoon, Build 201612091438-exported (Linux-x86_64))
usage: xinteract (generaloptions) (-Oprophetoptions) (-iiprophetoptions) (-Mptmprophetoptions) (-Xxpressoptions) (-Aasapoptions) (-L<conditionfile>libraoptions) xmlfile1 xmlfile2 ....
generaloptions:
For developers:
-t [run regression test against a previously derived result]
-t! [learn results for regression test]
-t# [run regression test, do not stop on test failure]
For users:
-Nmyfile.pep.xml [write output to file 'myfile.pep.xml']
-R fix protein names in OMSSA data
-G record collision energy in pepXML
-V record compensation voltage (FAIMS) in pepXML
-PREC record precursor intensity in pepXML
-nI [do not run Interact (convert to pepXML only)]
-nP [do not run PeptideProphet]
-nR [do not run get all proteins corresponding to degenerate peptides from database]
-p0 [do not discard search results with PeptideProphet probabilities below 0.05]
-x<num> [number of extra PeptideProphet interations; default <num>=20]
-I<num> [ignore charge <num>+]
-d<tag> [use decoy hits to pin down the negative distribution.
the decoy protein names must begin with <tag> (whitespace is not allowed)]
-D<database_path> [specify path to database]
-c<conservative_level> [specify how conservative the model is to be in number of standard deviations from negative mean
to allow positive model to cover (default 0, higher is more conservative)]
-PPM [use PPM instead of daltons in Accurate Mass Model]
-E<experiment_label> [used to commonly label all spectra belonging to one experiment (required by iProphet)]
-l<num> [minimum peptide length considered in the analysis (default 7)]
-T<database type> [specify 'AA' for amino acid, 'NA' for nucleic acid (default 'AA')]
-a<data_path> [specify absolute path to data directory]
-p<num> [filter results below PeptideProphet probability <num>; default <num>=0.05]
-mw [calculate protein molecular weights]
-MONO [calculate monoisotopic peptide masses during conversion to pepXML]
-AVE [calculate average peptide masses during conversion to pepXML]
-THREADS=<num> [specify maximum number of threads to use]
-eX [specify sample enzyme]
-eT [specify sample enzyme = Trypsin]
-eS [specify sample enzyme = StrictTrypsin]
-eC [specify sample enzyme = Chymotrypsin]
-eR [specify sample enzyme = RalphTrypsin]
-eA [specify sample enzyme = AspN]
-eG [specify sample enzyme = GluC]
-eB [specify sample enzyme = GluC Bicarb]
-eM [specify sample enzyme = CNBr]
-eD [specify sample enzyme = Trypsin/CNBr]
-e3 [specify sample enzyme = Chymotrypsin/AspN/Trypsin]
-eE [specify sample enzyme = Elastase]
-eK [specify sample enzyme = LysC / Trypsin_K (cuts after K not before P)]
-eL [specify sample enzyme = LysN (cuts before K)]
-eP [specify sample enzyme = LysN Promisc (cuts before KR)]
-eN [specify sample enzyme = Nonspecific or None]
PeptideProphet options [following the '-O']:
i [use icat information in PeptideProphet]
f [do not use icat information in PeptideProphet]
g [use N-glyc motif information in PeptideProphet]
H [use Phospho information in PeptideProphet]
m [maldi data]
I [use pI information in PeptideProphet]
R [use Hydrophobicity / RT information in PeptideProphet]
F [force the fitting of the mixture model, bypass automatic mixture model checks]
A [use accurate mass binning in PeptideProphet]
w [warning instead of exit with error if instrument types between runs is different]
x [exclude all entries with asterisked score values in PeptideProphet]
l [leave alone all entries with asterisked score values in PeptideProphet]
n [use hardcoded default initialization parameters of the distributions]
P [use Non-parametric model, can only be used with decoy option]
N [do not use the NTT model]
M [do not use the NMC model]
k [do not use the mass model]
o [optimize f-value function f(dot,delta) using PCA (applies only to SpectraST)]
G [use Gamma Distribution to model the Negatives (applies only to X!Tandem data)]
E [only use Expect Score as the Discriminant(applies only to X!Tandem data,
helpful for data with homologous top hits e.g. phospho or glyco)]
d [report decoy hits with a computed probability based on the model learned]
p [run ProteinProphet afterwards]
t [do not create png data plot]
u [do not assemble protein groups in ProteinProphet analysis]
s [do not use Occam's Razor in ProteinProphet analysis to
derive the simplest protein list to explain observed peptides]
iProphet options [run iProphet on the PeptideProphet result with options that follow the '-i']:
p [run ProteinProphet on the iProphet results]
P [do not use number of sibling peptides model]
R [do not use number replicate spectra model]
I [do not use number sibling ions model]
M [do not use number sibling mods model]
S [do not use numbe of sibling searches model]
E [do not use number of sibling MS/MS runs model]
PTMProphet options [run PTMProphet on the iProphet result with options that follow the '-M' (e.g. -M-STY,79.9663-MZTOL=0.4)]:
-{<amino acids, n, or c>,<mass_shift>,...} [specify mod masses (e.g. -STY,79.9663,K,114.0429,M,15.9949)]
-MZTOL=<number> [Use specified +/- mz tolerance on site specific ions (default=0.1 dalton)]
-NOUPDATE [Don't update modification_info tags in pepXML]
xpressoptions [will run XPRESS analysis with any specified options that follow the '-X']:
-m<num> change XPRESS mass tolerance (default=1.0)
-a tolerance specified by -m is in ppm (default=Daltons)
-n<str>,<num> change XPRESS residue mass difference for <str> to <num> (default=9.0)
-b heavy labeled peptide elutes before light labeled partner
-F<num> fix elution peak area as +-<num> scans (<num> optional, default=5) from peak apex
-c<num> change minimum number of chromatogram points needed for quantitation (default=5)
-p<num> number of 13C isotopic peaks to add to precursor chromatogram (default=1)
-L for ratio, set/fix light to 1, vary heavy
-H for ratio, set/fix heavy to 1, vary light
-M for 15N metabolic labeling; ignore all other parameters, assume
IDs are normal and quantify w/corresponding 15N heavy pair
-N for 15N metabolic labeling; ignore all other parameters, assume
IDs are 15N heavy and quantify w/corresponding 14N light pair
-O for 13C metabolic labeling; ignore all other parameters, assume
IDs are normal and quantify w/corresponding 13C heavy pair
-P for 13C metabolic labeling; ignore all other parameters, assume
IDs are 13C heavy and quantify w/corresponding 12C light pair
-i also export intensities and intensity based ratio
-l label free mode: stats on precursor ions only, no ratios
only relevant label-free parameters are -m, -c, and -p
asapoptions [will run ASAPRatio analysis with any specified options that follow the '-A']:
-l<str> change labeled residues (default='C')
-b heavy labeled peptide elutes before light labeled partner
-r<num> range around precusor m/z to search for peak (default 0.5)
-f<num> areaFlag set to num (ratio display option)
-S static modification quantification (i.e. each run is either
all light or all heavy)
-F use fixed scan range for light and heavy
-C quantitate only the charge state where the CID was made
-B return a ratio even if the background is high
-Z set all background to zero
-m<str> specified label masses (e.g. M74.325Y125.864), only relevant for
static modification quantification
libraoptions [will run Libra Quantitation analysis with any specified options that follow the '-L']:
refreshparser options (disabled by -nR switch)
-PREV_AA_LEN=<length> set the number of previous AAs recorded for a peptide hit (default 1)
-NEXT_AA_LEN=<length> set the number of following AAs recorded for a peptide hit (default 1)
-RESTORE_NONEXISTENT_IF_PREFIX=<str> for proteins which starts with <str> and not found in refresh database,
keep original protein names instead of NON_EXISTENT
examples:
xinteract *.pep.xml [combines together data in all pepXML files into 'interact.pep.xml', then runs PeptideProphet]
xinteract -Ndata.pep.xml *.pep.xml [same as above, but results are written to 'data.pep.xml']
xinteract -Ndata.pep.xml -X -Op *.pep.xml [same as above, but run XPRESS analysis in its default mode, then
ProteinProphet]
xinteract -X -A file1.pep.xml file2.pep.xml [combines together data in file1.pep.xml and file2.pep.xml into 'interact.pep.xml'
and then runs XPRESS (in its default mode) and ASAPRatio (in its default mode)]
xinteract -X-nC,6.0 -A file1.pep.xml file2.pep.xml [same as above, but specifies that cysteine label has a heavy/light
mass difference of 6.0]
xinteract -X -A-lDE-S file1.pep.xml file2.pep.xml [sampe as above, but specifies for ASAP to run in static mode
with labeled residues D and E]
xinteract -Lmyconditionfile.xml -Op file1.pep.xml file2.pep.xml [run libra quantitiation after PeptideProphet using myconditionfile.xml
Created
February 10, 2017 14:55
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xinteract_readme
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