1.4.2

Changes

• We have changed the internal settings of RawTools so output data files always use decimal dots rather than decimal commas (e.g. 1.234 vs 1,234). Previously decimal commas were sometimes the default depending on the system language. This decision was made because some database search engines are not able to properly parse MGF files with decimal commas. If this impacts your downstream workflow in a negative way, please let us know and we will try to make this change user-specified rather than a default.

Fixed

• There was a bug that resulted in crashes during quantification. This was introduced with the reporter mass error reporting. It has been fixed.
• MGF files in v1.4 were found to be incompatible with MS-GF+. This has been fixed.

RawToolsGUI-beta

RawToolsGUI is 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.

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.

1.4.1

This release fixes a bug in which RTINSECONDS, as reported in the MGF file, was actually in minutes.

1.4.0

Notable new features:

• Behind the scenes the workflow has been optimized, improving performance
• Automatic support for multiple processors
• Support for relative paths on the command line
• A new "logdump" feature has been added, which outputs the instrument log to a text file.

Please see the change log for more details and other changes.

1.4.0-beta

NOTE: This is a beta release. If you want the latest stable release look for v1.3.3. However, if you are looking for the newest features and fixes before they come out in the official release, then the beta is what you want. Be aware that new .zip files will appear under the Assets section as we add features and work out kinks. So to get the most recent version, look for the file with the largest number after "beta" in the title.

This release makes some significant changes to the processing workflow intended to improve performance, especially for large files (as in issue #6). This is a beta release. Feel free to try it out, but know there might be some bugs. If you find any, please let us know!

Also addressed in this release is issue #11. In that issue we note the number of scans reported is not always correct. This should be fixed here.

NOTE: When originally released, the .zip file available for download was actually a .tar file with the wrong extension. This has been fixed. [2018-12-04]

Changes

• RawTools-1.4.0-beta.3.zip Relative paths are now supported for all arguments.
• RawTools-1.4.0-beta.2.zip Precursor peaks are now extracted based on picked m/z rather than monoisotopic m/z.
• This release adds a new "logdump" function, which outputs the raw file instrument log to a text file. Use it like this:
  RawTools logdump -f [path to raw file]
RawTools logdump -d [directory in which to get log files from all raw files]
  Pretty much everything about how the instrument was operating is in there, scan by scan, from capillary temperature to lens voltages to turbopump lifetimes, etc.

Bugs found (in the beta) and fixed

• A column offset was introduced in MS3 Matrix files. This is fixed in RawTools-1.4.0-beta.5.zip [2019-01-03]
• MGF files were not compatible with MS Amanda. This is fixed in RawTools-1.4.0-beta.5.zip [2019-01-03]
• _Matrix files were not being generated when -q was used. This is fixed in RawTools-1.4.0-beta.4.zip [2018-12-20]
• Use of relative paths in QC arguments was resulting in duplicate nested folders for the QC output. This has been fixed in RawTools-1.4.0-beta.3.zip [2018-12-11]
• -N was being ignored during writing of MGF files for QC, resulting in all spectra being searched. This has been fixed in RawTools-1.4.0-beta.3.zip. [2018-12-11]
• RawTools-1.4.0-beta.zip has a bug where it crashes when it encounters an empty centroid stream. This has been fixed in RawTools-1.4.0-beta.1.zip [2018-12-05]
• Output matrix from parse ended in _parse.txt rather than _Matrix.txt. This has been fixed in RawTools-1.4.0.beta.2.zip [2018-12-07]

1.3.3

update app.config, version number

1.3.2

New examples section for command line interface (see >RawTools examples for info).
Several bug fixes. See changelog for details.

1.3.1

Some minor bug fixes in this release. See changelog for details.

1.3.0

This version of RawTools adds MS1 isolation interference calculation and refinement of precursor charge-state and monoisotopic mass. See changelog for further details.

1.2.0

This version of RawTools adds support for the X! Tandem search engine. See the changelog for more details on updates and changes.