The ThermoPeakDataExporter extracts peak intensity data from each scan in a Thermo .raw file, and writes that data to a tab-delimited text file.
ThermoPeakDataExporter reads data from Thermo .raw files using PNNL's Thermo Raw File Reader, which is a .NET DLL wrapper for Thermo's C#-based ThermoFisher.CommonCore DLLs. For more info, see https://github.com/PNNL-Comp-Mass-Spec/Thermo-Raw-File-Reader
ThermoPeakDataExporter.exe
ThermoRawFilePath [/O:OutputTSVFilePath]
[/MinInt:MinimumIntensity] [/MinRelInt:MinimumRelativeIntensity]
[/MinScan:ScanStart] [/MaxScan:ScanEnd]
[/MinMz:MzStart] [/MaxMz:MzEnd]
[/MinSN:MinimumSignalToNoiseRatio]
[/LoadMethod:True] [/LoadTune:True]
[/ParamFile:ParamFileName.conf] [/CreateParamFile]
The input file name must end in .raw
- Use wildcards to process multiple files, e.g.
*.raworQC*.raw - Can alternatively be a path to a directory with .raw files
The output file name is optional
- If omitted, the output file will be created in the same directory as the input file, but with extension .tsv.
- If processing a single file, this can alternatively be a path to an existing directory to create the .tsv file in a different directory than the .raw file
- When using wildcards, use
/Rto recursively search subdirectories
Use /MinInt to specify a minimum intensity threshold (absolute value)
Use /MinRelInt to specify a minimum relative intensity threshold (value between 0 and 100)
Use /MinScan and /MaxScan to limit the scan range of the exported data
Use /MinMz and /MaxMz to limit the m/Z range of the exported data
Use /MinSN to specify a minimum signal to noise ratio (minimum S/N)
Use /LoadMethod:False to disable loading the instrument method
- This can be useful for corrupt .raw files
Use /LoadTune:False to disable loading the tune data
- This can be useful for corrupt .raw files
The processing options can be specified in a parameter file using /ParamFile:Options.conf
- Define options using the format
ArgumentName=Value - Lines starting with
#or;will be treated as comments - Additional arguments on the command line can supplement or override the arguments in the parameter file
Use /CreateParamFile to create an example parameter file
- By default, the example parameter file content is shown at the console
- To create a file named Options.conf, use
/CreataParamFile:Options.conf
| Scan Number | RT | Mass | Intensity | Resolution | Baseline | Noise | Charge | SignalToNoise | RelativeIntensity |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 0.0037 | 212.074924 | 31783.9043 | 1355104 | 3.9968 | 43.2763 | 0 | 734.4418 | 8.2732 |
| 1 | 0.0037 | 212.075111 | 384180.9375 | 1297401 | 3.9968 | 43.2763 | 0 | 8877.3904 | 100 |
| 1 | 0.0037 | 213.078485 | 46274.5391 | 1247004 | 4.1086 | 43.627 | 0 | 1060.6848 | 12.045 |
| 1 | 0.0037 | 214.070926 | 20426.6836 | 1263700 | 4.2191 | 43.9739 | 0 | 464.5181 | 5.3169 |
| 1 | 0.0037 | 671.267394 | 23332.4785 | 366201 | 26.7497 | 82.0103 | 0 | 284.5067 | 6.0733 |
| 1 | 0.0037 | 681.296167 | 75601.5781 | 361001 | 26.9184 | 82.3053 | 0 | 918.5511 | 19.6786 |
| 1 | 0.0037 | 682.299526 | 27141.7754 | 363204 | 26.9352 | 82.3348 | 0 | 329.6515 | 7.0648 |
| 1 | 0.0037 | 733.267545 | 23193.8359 | 337901 | 27.7925 | 83.8339 | 0 | 276.6643 | 6.0372 |
| 2 | 3.0067 | 212.074926 | 31583.8809 | 1322904 | 3.0378 | 41.144 | 0 | 767.6425 | 8.2171 |
| 2 | 3.0067 | 212.07511 | 384368.7813 | 1299001 | 3.0379 | 41.1441 | 0 | 9342.024 | 100 |
| 2 | 3.0067 | 213.078487 | 47960.2578 | 1251504 | 3.1944 | 41.4723 | 0 | 1156.442 | 12.4777 |
| 2 | 3.0067 | 214.070929 | 20854.0293 | 1260400 | 3.3492 | 41.7969 | 0 | 498.9375 | 5.4255 |
| 2 | 3.0067 | 283.264308 | 20913.3262 | 881501 | 11.066 | 55.8397 | 0 | 374.5242 | 5.441 |
| 2 | 3.0067 | 447.134331 | 27278.0703 | 554704 | 18.6603 | 67.9551 | 0 | 401.413 | 7.0968 |
| 2 | 3.0067 | 671.26734 | 22926.4629 | 368101 | 24.8662 | 76.7817 | 0 | 298.5928 | 5.9647 |
| 2 | 3.0067 | 681.29613 | 58137.9414 | 364001 | 25.0193 | 77.0032 | 0 | 755.0072 | 15.1256 |
| 2 | 3.0067 | 682.299488 | 20715.3223 | 366804 | 25.0346 | 77.0253 | 0 | 268.9417 | 5.3894 |
| 2 | 3.0067 | 711.30667 | 22673.0352 | 350101 | 25.4775 | 77.6659 | 0 | 291.9305 | 5.8988 |
| 2 | 3.0067 | 733.267525 | 39559.2852 | 338201 | 25.8128 | 78.1508 | 0 | 506.1915 | 10.292 |
Written by Bryson Gibbons and Matthew Monroe for the Department of Energy (PNNL, Richland, WA)
E-mail: matthew.monroe@pnnl.gov or proteomics@pnnl.gov
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://panomics.pnnl.gov/ or https://www.pnnl.gov/integrative-omics
The ThermoPeakDataExporter is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause
Copyright 2018 Battelle Memorial Institute