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
mzML and indexed mzML
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.

Release Notes

You can read release notes (starting from version 1.1.7) in the wiki page

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 version of the executable.
  -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.
  -s, --stdout               Write to standard output. Cannot be combined with
                               file or directory output. Implies silent logging,
                                i.e. logging level 0
  -f, --format=VALUE         The spectra output format: 0 for MGF, 1 for mzML,
                               2 for indexed mzML, 3 for Parquet; both numeric
                               and text (case insensitive) value recognized.
                               Defaults to indexed mzML if no format is
                               specified.
  -m, --metadata=VALUE       The metadata output format: 0 for JSON, 1 for TXT;
                               both numeric and text (case insensitive) value
                               recognized
  -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[=VALUE]
                             Don't use the peak picking provided by the native
                               Thermo library. By default peak picking is
                               enabled. Optional argument allows disabling peak
                               peaking only for selected MS levels and should
                               be a comma-separated list of integers (1,2,3)
                               and/or intervals (1-3), open-end intervals (1-)
                               are allowed
  -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, 2 for default, 3 for warning, 4 for
                               error; both numeric and text (case insensitive)
                               value recognized.
  -e, --ignoreInstrumentErrors
                             Ignore missing properties by the instrument.
  -x, --excludeExceptionData Exclude 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
  -N, --noiseData            Include noise data in mzML output
  -w, --warningsAreErrors    Return non-zero exit code for warnings; default
                               only for errors
  -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

Output file extension is determined by the used output format and (optional) gzip compression, for example, if format is MGF without gzip compression, the output file will receive .mgf extension, if format is mzML with gzip compression the output file will have .mzML.gz extension. All user input will be standardized to fulfill abovementioned requrements.

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
  -w, --warningsAreErrors    Return non-zero exit code for warnings; default
                               only for errors
  -l, --logging=VALUE        Optional logging level: 0 for silent, 1 for
                               verbose, 2 for default, 3 for warning, 4 for
                               error; both numeric and text (case insensitive)
                               value recognized.

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 xic --help
  -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. Specify this or an output
                               file. Specifying neither writes to the input
                               directory.
  -b, --output_file=VALUE    The output file. Specify this or an output
                               directory. Specifying neither writes to the
                               input directory.
  -6, --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.
  -w, --warningsAreErrors    Return non-zero exit code for warnings; default
                               only for errors
  -l, --logging=VALUE        Optional logging level: 0 for silent, 1 for
                               verbose, 2 for default, 3 for warning, 4 for
                               error; both numeric and text (case insensitive)
                               value recognized.

Provide one of the following filters:

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

optionally one can define starting and ending retention times, provide filter string (defaults to ms, i.e. only MS1 scans), and a comment (free text) field; any valid filter string is supported, however only basic validation is performed, see issue #158 for details. Comment can contain any text and will be preserved in the output.

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
        },
        {
            "mz":1014.5099732499732,
            "rt_start":14.0600881872,
            "rt_end":14.4167198290667,
            "tolerance":5,
            "tolerance_unit":"ppm",
            "comment":"Only ion trap scans"
            "scan_filter":"ITMS"
        }
   }
]

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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

First check the latest version tag on biocontainers/thermorawfileparser/tags. Then pull and run the container with

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