RawTools
Kovalchik KA, Colborne S, Spencer SE, Sorensen PH, Chen DDY, Morin GB, et al. RawTools: Rapid and Dynamic Interrogation of Orbitrap Data Files for Mass Spectrometer System Management. J Proteome Res. 2018. doi:10.1021/acs.jproteome.8b00721
RawTools is a comprehensive and user-friendly software designed for the analysis of mass spectrometry-based proteomics data. It is an open-source tool that provides a range of features for processing and analyzing raw proteomics data, including quality control checks, filtering, normalization, peak detection, and quantification.
The tool supports various file formats commonly used in proteomics, including RAW, MGF, and mzML files, and offers a range of visualization options to aid in data exploration and interpretation. The software also includes advanced features such as label-free quantification, statistical analysis, and data normalization, making it an ideal tool for proteomics researchers.
One of the key strengths of RawTools is its user-friendly interface, which allows researchers to easily navigate through their data and perform complex analyses without the need for extensive programming skills. The software is regularly updated, and its development is driven by a community of researchers and bioinformaticians, ensuring that it stays up-to-date with the latest advancements in proteomics research.
Overall, RawTools is a powerful and versatile tool that can help researchers to efficiently process, analyze, and interpret their proteomics data, providing valuable insights into the biological systems under investigation.
More information is available in the Github repository.
Parameters
Here is the help text that explains the different parameters of RawTools that are relevant for Proteomics QC. However, not all of them were tested.
========== PARAMETERS HELP ==========
Below you will find information on all the parameters available to this application.
The Parameter field is a (hopefully) descriptive name of the parameter which might
be referenced when encountering an error. Short form and Long form are how you invoke
the parameters on the command line. You can use either form.
Required indicates whether the application requires the parameter have a value in order to run.
INFO DESCRIPTION ---------------
Parameter: RawFiles Indicates input file(s) to be processed, separated by a space if
Short form: -f there are multiple files. Must be Thermo .raw files. You must use
Long form: -files either -f or -d to indicate the file(s) to process.
Required: False
Parameter: Parse Parses raw file meta and scan data and writes the output to a
Short form: -p tab-delimited text file. Typically either this output or the
Long form: -parse quant output (-q) is used unless your aim is to simply create
an MGF or to observe broad metrics using -x.
Long form: -parse
Required: False
Parameter: Quant Similar to parse (-p), but also quantifies reporter ions and write
Short form: -q results to output matrix. Use of this flag requires you also specify
Long form: -quant the reagents used for isobaric labeling with the -r argument
Required: False (e.g. -r TMT10)
Parameter: LabelingReagent Required for reporter ion quantification. Reagents used to label
Short form: -r peptides, required if using quant option. Available options are:
Long form: -labellingreagent {TMT0, TMT2, TMT6, TMT10, TMT11, TMT16, iTRAQ4, iTRAQ8}.
Required: False
Parameter: UnlabeledQuant Calculate areas of precursor peaks and writes them to the parse or
Short form: -u quant file (ParentPeakArea column). This option is to be used in
Long form: -unlabeledquant combination with -p or -q.
Required: False
Parameter: WriteMGF Writes a standard MGF file. To specify a mass cutoff use the -c
Short form: -m argument.
Long form: -mgf
Required: False
Parameter: MgfMassCutoff Specify a mass cutoff to be applied when generating MGF files.
Short form: -c May be of use if removal of reporter ions is desired prior to
Long form: -masscutoff searching of MS2 spectra. Default is 0.
Required: False
Parameter: OutputDirectory The directory in which to write output. Can be a relative or
Short form: -o absolute path to the directory. If it is a relative path it
Long form: -out will be placed inside the directory containing the respective
Required: False raw file. Note that relative paths should not start with a slash.
If this is left blank the directory where the raw file is stored
will be used by default.
Parameter: Metrics Write a txt file containing general metrics about the MS run.
Short form: -x
Long form: -metrics
Required: False
Parameter: Chromatogram Write a chromatogram to disk. Should be in the format
Short form: -chro "-chro [order][type]", where order is the MS order (or a combination
Long form: -chromatograms of orders) and type is T, B, or TB (TIC, base peak and both,
Required: False respectively). For example, to generate MS1 and MS2 TIC and base
peak chromatograms, invoke "-chro 12TB". Or, to generate a MS2 TIC,
invoke "-chro 2T".
Parameter: RefineMassCharge Refine precursor charge and monoisotopic mass assignments.
Short form: -R Highly recommended if monoisotopic precursor selection was
Long form: -refinemasscharge turned off in the instrument method (or peptide match on a
Required: False QE instrument).
Parameter: MinCharge The minimum charge to consider when refining precursor
Short form: -min mass and charge.
Long form: -mincharge
Required: False
Parameter: MaxCharge The maximum charge to consider when refining precursor
Short form: -max mass and charge.
Long form: -maxcharge
Required: False
Parameter: FastaDB Required for an X! Tandem search during QC. Path to a
Short form: -db fasta protein database.
Long form: -fastadb
Required: False
Parameter: FixedModifications Fixed modifications to pass to the search, if desired.
Short form: -fmods Use mass@aminoacid1,mass@aminoacid2 format. It is important
Long form: -fixedmods that the values are separated with a comma and not spaces.
Required: False Invoke ">RawTools -modifications" to see examples of some
common modifications
Parameter: VariableModifications Variable modifications to pass to the search, if desired.
Short form: -vmods Use mass@aminoacid1,mass@aminoacid2 format. It is important
Long form: -variablemods that the values are separated with a comma and not spaces.
Required: False Invoke ">RawTools -modifications" to see examples of some
common modifications
Parameter: XTandemDirectory Specify the path to the X! Tandem directory (the directory
Short form: -X containing "tandem.exe") if you want to run a database search
Long form: -xtandem as part of QC.
Required: False
Parameter: NumberSpectra The number of MS2 spectra to be passes to the search engine as
Short form: -N an MGF file. Defaults to 10,000. If N is greater than the number
Long form: -numberspectra of MS2 scans in a raw file, all MS2 scans will be used.
Required: False
Parameter: LogDump Write the instrument logs from all provided raw files to disk.
Short form: -l
Long form: -logdump
Required: False