IdentiPy is a search engine for bottom-up proteomics written in Python.
IdentiPy is described in this JPR paper: http://dx.doi.org/10.1021/acs.jproteome.7b00640
Please cite it when using IdentiPy or its parts.
IdentiPy is published under the Apache 2.0 license.
pip install git+https://github.com/levitsky/identipy.git
or:
$ git clone https://github.com/levitsky/identipy
$ cd identipy
$ pip install .
See requirements.txt. Key dependencies are:
- Python
- scipy
- pyteomics
- lxml
- cython
- pyteomics.cythonize
You can separately install a web-based GUI for IdentiPy, IdentiPy Server. Please refer to the linked page for system requirements and installation instructions.
A typical command to process a file would look like this:
$ identipy -cfg my.cfg spectra.mgf
Here, my.cfg is a settings file specifying the search parameters. Allowed parameters and their default values are listed in the
default configuration file.
Settings not specified in my.cfg will be taken from the default file.
Search settings can also be overriden using command-line options.
For help on command-line usage, run:
$ identipy --help
You will see a message like this:
$ identipy --help
usage: identipy [-h] [-db FASTA] [-cfg CONFIG_FILE] [-out PATH] [-of FORMAT]
[-sep SEP] [-at] [-nopwide] [-punit UNIT] [-ptol VALUE]
[-lptol VALUE] [-rptol VALUE] [-funit UNIT] [-ftol VALUE]
[-fminmz VALUE] [-lmin N] [-lmax N] [-massmin VALUE]
[-massmax VALUE] [-e RULE] [-mc N] [-semi] [-noclip] [-cmin N]
[-cmax N] [-cumin N] [-cumax N] [-ime N] [-shifts SHIFTS]
[-snp SNP] [-rapid] [-mm N] [-ad] [-prefix PREFIX]
[-infix INFIX] [-method {reverse,shuffle}] [-deis]
[-deistol DEISTOL]
[-score {RNHS2,RNHS,hyperscore,morpheusscore}] [-minp N]
[-maxp N] [-dyn DYN] [-mfc N] [-nproc N] [-maxmods N]
[-ncleave NCLEAVE] [-ccleave CCLEAVE] [-fmods FMODS]
[-vmods VMODS] [-pmods PMODS] [-tags TAGS] [-debug]
[-dino DINO] [-dinoargs [DINOARGS ...]] [-demixing] [-pif]
file
Search proteins using LC-MS/MS spectra
positional arguments:
file input .mzML or .mgf file with MS/MS spectra
options:
-h, --help show this help message and exit
-db FASTA path to protein FASTA file
-cfg CONFIG_FILE path to file with parameters
-out PATH, -o PATH output path
-of FORMAT output format
-sep SEP output column separator (for table format)
-at Use auto-tuning of search parameters
-nopwide Do not increase initial precursor mass accuracy for
auto-tuning
-punit UNIT precursor mass tolerance unit
-ptol VALUE precursor mass tolerance
-lptol VALUE *left precursor mass tolerance
-rptol VALUE *right precursor mass tolerance
-funit UNIT fragment mass tolerance unit
-ftol VALUE fragment mass tolerance
-fminmz VALUE fragment min m/z
-lmin N min length of peptides
-lmax N max length of peptides
-massmin VALUE min mass of peptides
-massmax VALUE max mass of peptides
-e RULE cleavage rule in quotes!. X!Tandem style for cleavage
rules
-mc N number of missed cleavages
-semi include semitryptic peptides
-noclip Disable clipping of N-terminal methionine
-cmin N min precursor charge
-cmax N max precursor charge
-cumin N min unknown precursor charge
-cumax N max unknown precursor charge
-ime N precursor isotope mass error. The parent ion mass
tolerance is expanded by opening up multiple tolerance
windows centered on the given number of 13C isotope
peaks for a peptide.
-shifts SHIFTS shifts. example: 0,16.000,23.000,12
-snp SNP 1 means make SNP changes for ALL peptides
-rapid leave only 2000 random spectra for processing
-mm N number of minimum matched ions
-ad add decoy
-prefix PREFIX decoy prefix
-infix INFIX decoy infix
-method {reverse,shuffle}
decoy method; reverse or shuffle
-deis use MS/MS deisotoping
-deistol DEISTOL deisotope mass accuracy
-score {RNHS2,RNHS,hyperscore,morpheusscore}
used scoring function
-minp N minumum peaks in MS/MS spectra
-maxp N maximum peaks in MS/MS spectra
-dyn DYN dynamic range
-mfc N maximum fragment charge
-nproc N number of processes. 0 means auto
-maxmods N maximum variable mods per sequence
-ncleave NCLEAVE protein nterm cleavage
-ccleave CCLEAVE protein cterm cleavage
-fmods FMODS fixed modifications. Format:
mass1@aminoacid1,mass2@aminoacid2
-vmods VMODS variable modifications. Format:
mass1@aminoacid1,mass2@aminoacid2
-pmods PMODS variable protein terminal modifications
-tags TAGS Add quantitation tags to the pepXML output. Can be
tmt10plex, tmt6plex, tmt11plex or custom format
label1:mass1,label2:mass2...
-debug Print debugging messages
-dino DINO path to Dinosaur JAR file or Biosaur executable. Used
for chimeric spectrum processing and MS1 Intensity
calculation
-dinoargs [DINOARGS ...]
extra arguments to Dinosaur or Biosaur.
-demixing Use demixing
-pif Calculate PIF
Example usage
-------------
$ identipy input.mgf -db human.fasta
-------------
-
Pyteomics: https://github.com/levitsky/pyteomics
-
pyteomics.cythonize: https://github.com/mobiusklein/pyteomics.cythonize
-
IdentiPy Server: https://github.com/levitsky/identipy_server