Using lcmsWorld - PGB-LIV/lcmsWorld GitHub Wiki

Loading LC-MS data

From the file menu, choose 'Load LC-MS File' This loads LC-MS data from either a thermo.raw or PSI standard .mzml file. During the file load process, a new file (called .lcms) is created which allows lcmsWorld to quickly access portions of the data in future. The last used file can be loaded quickly either by selecting from the menu, or by pressing the F5 key; the file is then loaded and the last-used view is restored, typically, in around 1 second.

Viewing LC-MS data

Once the file loading has completed, an overview of the data is automatically on the screen. You can then rotate the displayed portion either left/right or up/down by holding the left mouse button and moving the mouse. The data can be viewed in more or less detail by using the mouse scroll wheel to zoom in or out. Different areas of the data can be viewed by holding the right mouse button. The functionality of the buttons can be swapped using a button at the bottom of the display, which is useful for touch-screen displays that emulate one mouse button. The 'View' menu allows a number of customisations of the viewpoint - including a low-value cutoff, the ability to superimpose m/z and retention time values on the screen, and dynamic rescaling of all three display axes independently.

Adding Identifications / Annotations

From the file menu, choose 'Load Identifications'. This loads identification / annotation information from PSI-standard .mztab, .mzidentml, or correctly formatted .csv or .txt (tab-delimited) files. The minimum requirement is that the identifical files contain, for each point, an identifier, a m/z value and and retention time value. We have found that .mztab files often omit the optional retention time information, and these cannot be viewed in lcmsWorld.

Viewing Identifications / Annotations

There are three ways to view annotations; Firstly selecting 'show closest annotation' from the Annotations menu will show the closest annotation to the current cursor as a box on-screen with the accompanying label. Further information about this annotation is displayed in the Information Panel - inclduing the full label name, the exact m/z and retention time values and the reported protein and ptm, if these are present in the annotations file. The 'mark annotations' option allows a radius around every annotation to be highlighted in red - this gives a quick indication of how much of the input file has been identified. Annotations can also be found by selecting the name from the dropdown list. This can be filtered either by a text string matching the name, or one matching a given protein name. Selecting the checkbox for each annotation name will add a box and label to the data display on the annotation. Selecting the annotation name directly will automatically zoom the viewpoint to focus on the selected annotation.

Comparing Files

To compare multiple files simultaneously, it is possible to startup multiple instances of lcmsWorld - either directly from the desktop or by choosing 'Start New Instance' from the file menu. Enabling the 'Share Camera Controls' option from the 'View' menu will allow each of these instances to load a different data file, but to all view the same m/z and retention time area at the same time. By holding the 'alt' key when holding the right mouse button, you can adjust the centering of each display independently, which may be of use in comparing data files which have different retention time alignments.