PyCAMVerter

Utility for converting searched mass spec data into a format readable by CAMV.

Installation

To download a completely packaged Windows executable, visit our releases page

To install the core pycamverter python library, install the latest version of pip and run the following command:

pip install pycamverter

If you are running PyCAMVerter on a non-Windows system, you will need to install Docker and download the following package to read raw spectra data:

docker pull chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:x64

Usage

To use pycamverter, select your raw data file, your search files (Proteome Discoverer .msf), and an optional excel listing scan numbers in a file browser. Then simply drag-and-drop them onto PyCAMVerter.exe.

After a few minutes of processing, you should see the output .camv.gz file in the same directory as your raw file.

For a full list of arguments, run PyCAMVerter.exe from the command line:

usage: PyCAMVerter [-h] [-v] [-q] [-V] [--cpus CPUS] [--reprocess]
                   [--no-auto-maybe] [--raw-paths RAW_PATHS [RAW_PATHS ...]]
                   [--search-path SEARCH_PATH] [--scans-path SCANS_PATH]
                   [--scans [SCANS [SCANS ...]]] [--score SCORE]
                   [--mat-sessions MAT_SESSIONS [MAT_SESSIONS ...]]
                   [--out-path OUT_PATH]
                   [files [files ...]]

positional arguments:
  files                 Raw, search, or scan list files, determined by file
                        extension.

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         Increase verbosity of output.
  -q, --quiet           Decrease verbosity of output.
  -V, --version         show program's version number and exit
  --cpus CPUS           Limit the number of concurrent processes.
  --reprocess           Reprocess a set of scans, without limiting ptm
                        combinations.
  --no-auto-maybe       Don't auto-assign all peptides with best MASCOT rank
                        as 'maybe'
  --raw-paths RAW_PATHS [RAW_PATHS ...]
                        Raw data file(s) containing mass spec data.
  --search-path SEARCH_PATH
                        MASCOT or ProteomeDiscoverer search files.
  --scans-path SCANS_PATH
                        .xlsx or .csv file listing scans to select for
                        validation.
  --scans [SCANS [SCANS ...]]
                        Individual scans to select for validation.
  --score SCORE         Minimum Ion Score to include for validation.
  --mat-sessions MAT_SESSIONS [MAT_SESSIONS ...]
                        Path to CAMV-Matlab session files.
  --out-path OUT_PATH   Output path for CAMV export.