raw2ms2

Command-line tool that converts the raw experimental MS/MS data to the MS2 format. This tool is a Linux wrapper for the ProteoWizard’s msconvert tool and requires docker to be installed to run. Please see this for additional information. HiCOPS only supports the MS2 format as of now thus, all data must be converted to MS2 before using with HiCOPS.

Note: If you are working on a Windows machine, please use the msconvert tool directly and not use this docker based tool for better performance.

General Syntax

$ sudo HICOPS_INSTALL/tools/ms2prep/raw2ms2 [fmt] [absolute/path/to/data*.fmt|.FMT]

Paramaters:

• fmt: The file format of the input experimental data. For example: raw, mzML. Default: raw.
• abs_path: Absolute path to the folder where the data.fmt or data.FMT are located.

Example Usage

$ sudo HICOPS_INSTALL/tools/ms2prep/raw2ms2 mgf /disk/raptor-2/mhase003/datasets/test/
Using default tag: latest
latest: Pulling from chambm/pwiz-skyline-i-agree-to-the-vendor-licenses
Digest: sha256:f0f70674df9f180f45607ecd8500ca9ca0d091b251fca9ab1cd8710de8fa5132
Status: Image is up to date for chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:latest
format: MS2
outputPath: /disk/raptor-2/mhase003/datasets/test//converted
extension: .ms2
contactFilename:
runIndexSet:

spectrum list filters:

chromatogram list filters:

filenames:
  /disk/raptor-2/mhase003/datasets/test//14Sep18_Olson_S01.mgf

processing file: /disk/raptor-2/mhase003/datasets/test//14Sep18_Olson_S01.mgf
calculating source file checksums
writing output file: /disk/raptor-2/mhase003/datasets/test//converted\14Sep18_Olson_S01.ms2