ThermoRawFileParser

Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono (works on Windows too). It takes a thermo RAW file as input and outputs a metadata file and the spectra in 3 possible formats:

MGF: MS2 and MS3 spectra
mzML and indexed mzML: MS1, MS2 and MS3 spectra
Apache Parquet: under development

As of version 1.2.0, 2 subcommands are available (shoutout to the eubic 2020 developers meeting, see usage for examples):

query: returns one or more spectra in JSON PROXI by scan number(s)
xic: returns chromatogram data based on JSON filter input

These features are still under development, remarks or suggestions are more than welcome.

ThermoRawFileParser Publication:

Hulstaert N, Shofstahl J, Sachsenberg T, Walzer M, Barsnes H, Martens L, Perez-Riverol Y: ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion [PMID 31755270].
If you use ThermoRawFileParser as part of a publication, please include this reference.

(Linux) Requirements

Mono (install mono-complete if you encounter "assembly not found" errors).

Download

Click here to go to the release page (with release notes starting from v1.1.7).

You can find the ThermoRawFileParserGUI here.

Usage

mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw -o=/home/user/data_input/output/ -f=0 -g -m=0

with only the mimimal required argument -i or -d this becomes

mono ThermoRawFileParser.exe -i=/home/user/data_input/raw_file.raw

mono ThermoRawFileParser.exe -d=/home/user/data_input/

For running on Windows, omit mono. The optional parameters only work in the -option=value format. The tool can output some RAW file metadata -m=0|1 (0 for JSON, 1 for TXT) and the spectra file -f=0|1|2|3 (0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet) or both. Use the -p flag to disable the thermo native peak picking.

ThermoRawFileParser.exe --help
 usage is ThermoRawFileParser.exe [subcommand] [options]
optional subcommands are xic|query (use [subcommand] -h for more info]):
  -h, --help                 Prints out the options.
      --version              Prints out the library version.
  -i, --input=VALUE          The raw file input (Required). Specify this or an
                               input directory -d.
  -d, --input_directory=VALUE
                             The directory containing the raw files (Required).
                               Specify this or an input raw file -i.
  -o, --output=VALUE         The output directory. Specify this or an output
                               file -b. Specifying neither writes to the input
                               directory.
  -b, --output_file=VALUE    The output file. Specify this or an output
                               directory -o. Specifying neither writes to the
                               input directory.
  -f, --format=VALUE         The spectra output format: 0 for MGF, 1 for mzML,
                               2 for indexed mzML, 3 for Parquet. Defaults to
                               mzML if no format is specified.
  -m, --metadata=VALUE       The metadata output format: 0 for JSON, 1 for TXT.
  -c, --metadata_output_file=VALUE
                             The metadata output file. By default the metadata
                               file is written to the output directory.
  -g, --gzip                 GZip the output file.
  -p, --noPeakPicking        Don't use the peak picking provided by the native
                               Thermo library. By default peak picking is
                               enabled.
  -z, --noZlibCompression    Don't use zlib compression for the m/z ratios and
                               intensities. By default zlib compression is
                               enabled.
  -a, --allDetectors         Extract additional detector data: UV/PDA etc
  -l, --logging=VALUE        Optional logging level: 0 for silent, 1 for
                               verbose.
  -e, --ignoreInstrumentErrors
                             Ignore missing properties by the instrument.
  -x, --includeExceptionData Include reference and exception data
  -L, --msLevel=VALUE        Select MS levels (MS1, MS2, etc) included in the
                               output, should be a comma-separated list of
                               integers ( 1,2,3 ) and/or intervals ( 1-3 ),
                               open-end intervals ( 1- ) are allowed
  -P, --mgfPrecursor         Include precursor scan number in MGF file TITLE
  -u, --s3_url[=VALUE]       Optional property to write directly the data into
                               S3 Storage.
  -k, --s3_accesskeyid[=VALUE]
                             Optional key for the S3 bucket to write the file
                               output.
  -t, --s3_secretaccesskey[=VALUE]
                             Optional key for the S3 bucket to write the file
                               output.
  -n, --s3_bucketName[=VALUE]
                             S3 bucket name

A (java) graphical user interface is also available here that enables the selection of an input RAW directory or one ore more RAW files.

query subcommand

Enables the retrieval spectra by (a) scan number(s) in PROXI format.

mono ThermoRawFileParser.exe query -i=/home/user/data_input/raw_file.raw -o=/home/user/output.json n="1-5, 20, 25-30"

ThermoRawFileParser.exe query --help
usage is:
  -h, --help                 Prints out the options.
  -i, --input=VALUE          The raw file input (Required).
  -n, --scans=VALUE          The scan numbers. e.g. "1-5, 20, 25-30"
  -b, --output_file=VALUE    The output file. Specifying none writes the output
                               file to the input file parent directory.
  -p, --noPeakPicking        Don't use the peak picking provided by the native
                               Thermo library. By default peak picking is
                               enabled.
  -s, --stdout               Pipes the output into standard output. Logging is
                               being turned off.

xic subcommand

Return one or more chromatograms based on query JSON input.

mono ThermoRawFileParser.exe xic -i=/home/user/data_input/raw_file.raw -j=/home/user/xic_input.json

ThermoRawFileParser.exe query --help
usage is:
  -h, --help                 Prints out the options.
  -i, --input=VALUE          The raw file input (Required). Specify this or an
                               input directory -d
  -d, --input_directory=VALUE
                             The directory containing the raw files (Required).
                               Specify this or an input file -i.
  -j, --json=VALUE           The json input file (Required).
  -p, --print_example        Show a json input file example.
  -o, --output=VALUE         The output directory. If not specified, the output
                               is written to the input directory
  -b, --base64               Encodes the content of the xic vectors as base 64
                               encoded string.
  -s, --stdout               Pipes the output into standard output. Logging is
                               being turned off.

Provide one of the following filters:

M/Z and tolerance (tolerance unit optional, default ppm)
M/Z start and end
sequence and tolerance (tolerance unit optional, default ppm)

with optional parameters start en end retention time and filter (thermo filter string, defaults to ms)

An example input JSON file:

[
        {
            "mz":488.5384,
            "tolerance":10,
            "tolerance_unit":"ppm"           
        },
        {
            "mz":575.2413,
            "tolerance":10,
            "rt_start":630,
            "rt_end":660,
            "scan_filter":"ms2"
        },
        {
            "mz_start":749.7860,
            "mz_end" : 750.4,            
            "rt_start":630,
            "rt_end":660
        },
        {
            "sequence":"TRANNEL",
            "tolerance":10
        }
]

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Galaxy integration

ThermoRawFileParser is available in the Galaxy ToolShed and is deployed at the European Galaxy Server.

Logging

By default the parser only logs to console. To enable logging to file, uncomment the file appender in the log4net.config file.

<log4net>
    <root>
        <level value="INFO" />
        <appender-ref ref="console" />
        <!--<appender-ref ref="file" />-->
    </root>
    <appender name="console" type="log4net.Appender.ConsoleAppender">
        <layout type="log4net.Layout.PatternLayout">
            <conversionPattern value="%date %level %logger - %message%newline" />
        </layout>
    </appender>
    <!--<appender name="file" type="log4net.Appender.RollingFileAppender">
        <file value="ThermoRawFileParser.log" />
        <appendToFile value="true" />
        <rollingStyle value="Size" />
        <maxSizeRollBackups value="5" />
        <maximumFileSize value="10MB" />
        <staticLogFileName value="true" />
        <layout type="log4net.Layout.PatternLayout">
            <conversionPattern value="%date [%thread] %level %logger - %message%newline" />
        </layout>
    </appender>-->
</log4net>

Docker

Run ThermoRawFileParser simply with the pre-build biocontainer:

docker run -i -t -v /home/user/raw:/data_input quay.io/biocontainers/thermorawfileparser:1.1.2--0 ThermoRawFileParser.sh --help

Basic docker

Use the Dockerfile_basic docker file to build an image. It fetches to source code from github and builds it.

docker build --no-cache -t thermorawparser -f Dockerfile_basic .

Run example:

docker run -v /home/user/raw:/data_input -i -t thermorawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0

Create example for reusing the container:

docker create -v /home/user/raw:/data_input --name=rawparser -it thermorawparser
docker start rawparser
docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
docker exec rawparser mono /src/bin/x64/Debug/ThermoRawFileParser.exe -i=/data_input/another_raw_file.raw -o=/data_input/output/ -f=0 -g -m=0
docker stop rawparser

Biocontainers docker

Use the Dockerfile docker file to build an image. It fetches to source code from github and builds it.

docker build --no-cache -t thermorawparser .