Labeled LC-MS/MS Workflow

This is a tutorial for processing LC/MSMS data files through El-MAVEN. Convert files to mzml/mzxml format using msConvert

Contents

  • Preprocessing
  • Launch El-MAVEN
  • Adjust Global Settings
  • Load Samples
  • Load Compound Database
  • Mark Blanks
  • Alignment
  • Peak Grouping
  • Baseline
  • Mass Spectra
  • Peak Curation
  • Guidelines for Peak Picking
  • Export options

Preprocessing

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:

Screenshot 1

NOTE: It is important that Zlib compression is enabled by default in msConvert. El-MAVEN 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 El-MAVEN primarily uses .mzXML and .mzML formats.

Launch El-MAVEN

Once sample files are ready for processing, launch El-MAVEN.

Screenshot 2

Adjust Global Settings

Global Settings can be changed from the Options dialog (Insert icon). There are 9 tabs in the dialog. Each of these tabs has parameters related to a different module in El-MAVEN. For example, a tab for Instrumentation details, a tab for file import settings, et cetera.

Screenshot 3

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.

Load Samples

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.

Screenshot 4

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. El-MAVEN automatically assigns a color to every sample. User can select/deselect any sample by clicking the checkbox on the left of the sample name.

Screenshot 5

Load Compound Database

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.

Screenshot 6

This is a sample Compound Database:

Screenshot 7

It lists all metabolite names, chemical formula, HMDB ID, and the class/category of compounds they belong to (if known).

Mark Blanks

The user can mark the blanks by selecting the blank samples from the list on screen, and clicking on the Set as a Blank Sample icon (Insert icon) in Samples menu.

Screenshot 8

Multiple blanks can be marked together. The blanks will appear black as shown in the image below:

Screenshot 9