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 was just accepted for the Journal of Proteome Research special issue on Software Tools and Resources, here. The RawTools original manuscript preprint is available on bioRxiv.

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

If you need help installing and using RawTools, please visit the wiki page appropriate for your system and follow the instructions outlined here.

This new beta release adds a graphical user interface to RawTools. It runs on top of a modified version of RawTools 1.4.1, and provides a user-friendly interface to set up all your parse and search parameters. RawToolsGUI then formats the proper command line arguments and runs a new instance of RawTools for you using those arguments. You can save and load the parameters as well, so once you have a standard routine set up, you won't need to click so many buttons every time you want to run it.

The release includes regular RawTools as well, so there is no need to copy any files around. Once we are ready to move past the beta stage, RawToolsGUI will simply be incorporated into the regular RawTools distribution. You will be able to run RawTools with the CLI using RawTools.exe and as a GUI using RawToolsGUI.exe, but both files will be distributed in all releases.

if you are using RawToolsGUI and have any issues or suggestions let us know!

NOTE RawToolsGUI, like RawTools, requires the .NET or Mono Framework. This means if you are running from Linux or Mac you will still need to run it from a console like this: $ mono RawToolsGUI.exe. At some point we plan to include a simple console script that will do this for you when you click on it.

• A RawTools GUI is in the works and should be released soon! Initially this will simply allow you to set up RawTools parameters and run the program using a graphical interface instead of the command line. In the future we plan to add some basic features to visualy explore raw files, as well as to visualize some of the parse and QC data similar to our R Shiny app. If you have any features you would like to see in this regard, let us know by creating a feature request! [2019-01-07]

• Thanks to a lot of behind the scenes work, the file downloads of plots from the Shiny app are now working! [2018-12-06]

• The R Shiny application now has greater support for plot customisation. We have also added the ability to highlight points on QC plots. Lastly, we have added a new 'multi-plot' page where multiple scan matrix files can be input at once and plots for all files will be generated alongside one another in the same space. The latest version is live on the web and available here. [2018-11-29]

• The Shiny application has been updated to allow downloading of pdf versions of the created plots. These images can be imported to programs like Adobe Illustrator and will be treated as vector images. We have also added the ability to mouseover data points to see values, as well as corrected some bugs. We have also added the ability to add mean and median lines to the QC plots. The latest Shiny web interface is available here. [2018-11-07]

• 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]

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.

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.

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.

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.

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

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.