ThermoRawFileParser

By default, the parser only logs to the console. To enable logging to a file, you must modify the log4net.config file to uncomment the file appender section.

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

The xic subcommand requires a JSON array of query objects. Each object can define different types of filters.

Supported Filter Types:

1. M/Z and tolerance: Use mz and tolerance (defaults to ppm).
2. M/Z range: Use mz_start and mz_end.
3. Sequence: Use sequence and tolerance (defaults to ppm).
4. Retention Time: Use rt_start and rt_end.
5. Scan Filter: Use scan_filter (e.g., ms2, ITMS).
6. Comment: A free text field preserved in the output.

Example JSON structure:

[
    {
        "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"
    }
]

The xic subcommand returns one or more chromatograms based on a JSON input file. The JSON file can contain filters for M/Z (with tolerance), M/Z ranges, or peptide sequences (with tolerance). You can also define retention time (RT) ranges and scan filters.

XIC Subcommand Options:

• -i, --input=VALUE: Required. The raw file input.
• -j, --json=VALUE: Required. The JSON input file containing queries.
• -b, --output=VALUE: The output file.
• -o, --output_directory=VALUE: The output directory.
• -6, --base64: Encodes xic vectors as base64 strings.
• -p, --print_example: Show a JSON input file example.
• -s, --stdout: Pipe output to standard output.
• -w, --warningsAreErrors: Return non-zero exit code for warnings.
• -l, --logging=VALUE: Logging level (0-4).

# Run XIC extraction using a JSON query file
ThermoRawFileParser.exe xic -i=/home/user/data_input/raw_file.raw -j=/home/user/xic_input.json

The main executable accepts several options for controlling file conversion, output formats, and extraction details. Note that optional parameters must use the -option=value format.

Core Options:

• -h, --help: Prints help.
• -v, --version: Prints version.
• -i, --input=VALUE: Required. The raw file input.
• -d, --input_directory=VALUE: Required. The directory containing raw files.
• -b, --output=VALUE: The output file.
• -o, --output_directory=VALUE: The output directory.
• -s, --stdout: Write to standard output (implies silent logging).

Format Options:

• -f, --format=VALUE: Spectra output format. 0 for MGF, 1 for mzML, 2 for indexed mzML, 3 for Parquet, 4 for None. Defaults to indexed mzML.
• -m, --metadata=VALUE: Metadata format. 0 for JSON, 1 for TXT, 2 for None. Defaults to None.
• -c, --metadata_output_file=VALUE: Specific metadata output file path.
• -g, --gzip: GZip the output file.
• -z, --noZlibCompression: Disable zlib compression for m/z and intensities.

Extraction & Filtering:

• -p, --noPeakPicking[=VALUE]: Disable native Thermo peak picking. Can accept a comma-separated list of integers or intervals (e.g., 1,2,3 or 1-3 or 1-).
• -L, --msLevel=VALUE: Select MS levels (e.g., 1,2,3 or 1-3).
• -a, --allDetectors: Extract additional detector data (UV/PDA etc).
• -x, --excludeExceptionData: Exclude reference and exception data.
• -N, --noiseData: Include noise data in mzML output.
• -C, --chargeData: Include instrument detected charge states in mzML.

Advanced & Cloud:

• -u, --s3_url[=VALUE]: Write directly to S3.
• -k, --s3_accesskeyid[=VALUE]: S3 access key.
• -t, --s3_secretaccesskey[=VALUE]: S3 secret key.
• -n, --s3_bucketName[=VALUE]: S3 bucket name.

Logging & Errors:

• -l, --logging=VALUE: Level: 0 (silent), 1 (verbose), 2 (default), 3 (warning), 4 (error).
• -w, --warningsAreErrors: Return non-zero exit code for warnings.