RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files.
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README.md

RawTools

Welcome to the RawTools page! RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files. RawTools is written in C# and uses the Thermo RawFileReader library. RawTools is fully compatible with Windows, Linux, and MacOS operating systems. RawTools is the replacement for the previously described RawQuant Python package.

The RawTools manuscript preprint is available on bioRxiv.


RawTools releases

To obtain the latest compiled release of RawTools or to obtain an older version, please visit the Releases page.


Notable news

  • The Shiny application is now back online here. [2018-10-01]

  • The RawTools Shiny application has been revamped to use a new interface and to provide functionality for plotting of 'Matrix' and 'chromatogram' outputs. Matrix files are generated using the RawTools parse functionality and can be useful for visualizing data temporally across the acquisition. Chromatogram files are also generated using the parse functionality, with the --chro flag. The new application is currently available on GitHub from here. The web page can be accessed from this link. [2018-09-26]

  • RawTools now offers support for X! Tandem in as a search engine to facilitate calculation of identification-related metrics. IdentiPy remains available and the user may decide which search engine they wish to use. We are working on updating the help documentation to reflect this addition. [2018-09-24]


Getting help

If you need help getting started with RawTools or with understanding the output, please visit the RawTools Wiki.

If you have noticed an error in RawTools or have an idea for a new feature, please make a post on the Issues page.


RawTools R Shiny page

If you are just here looking for the web application page for visualizing your quality control results: RawTools R Shiny web application. You can also download the application from here for local use on your own machine.


Staying up to date

If you want to see what features we have in mind or are actively working on integrating into RawTools, visit the Projects page for more details.


Modifying RawTools

If you want to modify the RawTools source code, you will need to get a copy of RawFileReader from ThermoFisher. Otherwise the project will not have access to RawFileReader and you won't be able to debug or compile any code you write. You need to request access to Thermo Fisher's file share site to do this. It is a pretty simple process: you just need to email and request access. Details for access and subsequent installation of the package in Visual Studio can be found on the RawFileReader page on planetorbitrap.com.

Please make note of and respect the RawFileReader license in any modifications you make and wish to distribute.


License and copyright

RawTools (Copyright 2018 Kevin Kovalchik & Christopher Hughes) is licensed under Apache 2.0


Third-party licenses and copyright

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved. See RawFileReaderLicense for licensing information. Note: anyone recieving RawFileReader as part of a larger software distribution (in the current context, as part of RawTools) is considered an "end user" under section 3.3 of the RawFileReader License, and is not granted rights to redistribute RawFileReader.

CommandLineParser. Copyright 2005-2018 Giacomo Stelluti Scala & Contributors. See CommandLineParserLicense for licensing information.

Serilog. Copyright 2013-2015 Serilog Contributors. See SerilogLicense for licensing information.