Labeled MRM Workflow
This is a tutorial for processing LC/MSMS data files through ElMaven.
msConvert is a command-line/ GUI tool that is used to convert between various mass spectroscopy data formats, developed and maintained by proteoWizard.
Input
msConvert supports the following formats:
- .mzXML
- .mzML
- .RAW Thermofisher
- .RAW Walters
- .d Agilent
- .wiff format ABSciex
The settings used for msConvert as a GUI tool are captured in the following screenshots:
NOTE: It is important that Zlib compression is enabled by default in msConvert. ElMAVEN in its current form does not support Zlib compression. Make sure to uncheck "Use Zlib compression" box.
Output
msConvert can convert to an array of different formats but ElMaven primarily uses .mzXML and .mzML formats.
Global Settings can be changed from the Options dialog . User will find different tabs like Instrumentation, File Import, Peak Detection, Isotope Detection etc.
To know more about the functionality of different tabs and their settings, user can see the Widgets page. Please be sure to set the desired settings before processing an input file.
User can go to File in the Menu, click on Load Samples|Projects|Peaks option in the File menu. Then navigate to the folder containing the sample data, select all .mzXML or .mzml files and click Open. A loading bar displays the progress at the bottom.
When the samples have loaded, user should see a sample panel on the left side. If it is not displayed automatically, click on the Show Samples Widget button on the toolbar. ElMaven automatically assigns a color to every sample. User can select/deselect any sample by clicking the checkbox on the left of the sample name.
User can click on Compounds option in the leftmost menu, navigate to the folder containing the standard database file, select the appropriate .csv file and click Open.
This is a sample Compound Database:
It lists polarity/ionization mode, metabolite & fragment information, m/z of precursor ion, m/z of product ion, and expected Retention Time of compounds.
Marking Blanks
The user can mark the blanks by selecting the blank samples from the list on screen, and clicking on the Petri Dish icon in Samples menu.
Multiple blanks can be marked together. The blanks will appear black as shown in the image below:
(missing)
There are multiple export options available for storing marked peak data. User can either generate a PDF report to save the EIC for every metabolite, export data for a particular group in .csv format, or export the EICs to a Json file as shown below.
User can select All, Good, Bad or Selected peaks to export.
The Export Groups to CSV option lets the user save the 'good'/'bad' labels along with the peak table. User also has the option to filter out rows that have a certain label while exporting the table. Another option is to export the peak data in .mzroll format that can be directly loaded into ElMaven by clicking on the Load Samples|Projects|Peaksoption in the File menu. For this, user go the File option in the menu bar, and click on 'Save Project'.
