ms2view - a simple mass spectrum viewer with vim-like bindings

SYNOPSIS

ms2view --raw input.mzML [--pepxml ids.pepxml ...etc...]

DESCRIPTION

ms2view is a simple viewer for tandem mass spectrometry data. It combines an overview of an LC-MS/MS run with display of individual MS1 and MS2 spectra. It can also show and annotate peptide spectral matches based on pepXML or tab-delimited input.

While navigation can be done using a mouse, there is also a set of vim-like keybindings to allow quick navigation via the keyboard. The supported bindings are described below.

PREREQUISITES

Requires the following non-core Perl libraries:

• Gtk3
• Gtk3::SimpleList
• MS

COMMAND-LINE OPTIONS

• --raw filename

  Path to input mzML file (required)

• --pepxml filename

  Path to input pepXML containing spectral IDS for the corresponding mzML

• --ids filename

  Path to input tab-separated table containing spectral IDS for the corresponding mzML

• --hardklor

  Path to Hardklor output file containing peptide features for the corresponding mzML (NOTE: this feature is currently unimplemented)

KEY BINDINGS

The following keybindings are enabled:

• tab switch focus between three main canvases
• h l move peak selection left and right respectively (if the overview panel is in focus, this will move to the next MS1 scan and load it in the spectrum window)
• H L zoom canvas out and in on x-axis (zoom centers on currently selected peak)
• J K zoom canvas out and in on y-axis
• <numberg> center the canvas at the m/z coordinate given by <number>
• s save the currently focused canvas as PNG (will prompt for filename)

MOUSE NAVIGATION

The following mouse actions are supported on each spectrum canvas:

• left-click change the current peak selection. The selected peak will be the one with apex closest to the click point in Euclidean space.
• shift+left-click drag to select a window and add an m/z label to the most intense peak in the selected window
• ctrl+left-click drag from near the apex of one peak to the apex and another to display an on-screen ruler of the horizontal distance in m/z
• right-click drag to move canvas view horizontally
• scroll-wheel change x-axis zoom
• ctrl+scroll-wheel change y-axis zoom

CAVEATS AND BUGS

Please submit bug reports to the issue tracker in the distribution repository.

AUTHOR

Jeremy Volkening

LICENSE AND COPYRIGHT

Copyright 2014-24 Jeremy Volkening

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.