In ELELAB/lipidQ: Lipidomics Analysis Tool

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Introduction

The global options operation tab in the LipidQ GUI makes it possile to create both databases and user specified column names templates, when the user needs to have a new version. There can be several reasons why the user wishes to do so. Here are the two most common ones:

1. If the file has been corrupted, e.g. by typing in errors in the templates, which makes them unusuable, the user can re-create a template and start over, if the source of the corruption can not be found by manual inspection.

2. If the user has more than one project with different settings, the user can create a template for each project. It is recommended to save the files at different locations so that the template file is not overwritten. The best practice is to have a folder for each project.

Create Database templates

In order to create/reset a user specified column names template file, the user simply needs to do the following four steps:

1. Specify which database type to create (endogene database or ISTD database)

2. Import the user specified column names file for the project, so that the new database will have these column names.

3. Specify the path to where the template file should be saved

4. Press 'Create column template file'

Create column names template file

In order to create/reset a user specified column names template file, the user simply needs to do the following three steps:

1. Specify the number of MS2 columns

In order to specify the number of MS2 columns, the user needs to consider only the different MS2 names and not MS2 column names that belongs to a specific MS2 name. For instance, for the following columns:

"MASSFRAG1", "FRAG1.mE504_POS_01.raw", "FRAG1.mE504_POS_02.raw"

"MASSFRAG2", "FRAG2.mE504_POS_01.raw", "FRAG2.mE504_POS_02.raw"

"MASSFA1", "FA1.mE504_POS_01.raw", "FA1.mE504_POS_02.raw"

"MASSFA2", "FA2.mE504_POS_01.raw", "FA2.mE504_POS_02.raw"

, the number of MS2 columns is 4, since columns such as MASSFRAG1, FRAG1.mE504_POS_01.raw, and FRAG1.mE504_POS_02.raw all belongs to FRAG1, columns such as MASSFRAG2, FRAG2.mE504_POS_01.raw, and FRAG2.mE504_POS_02.raw all belongs to FRAG2 and so on. The maximum numbers of MS2 columns defined in this way can not exceed 20.

2. Specify the path to where the template file should be saved

next, the folder where the output files should be saved to has to be defined in the "Paste the filepath for the column template file to be saved" field. Here we'll write the filepath to where we wish to save the files. The following describes how to obtain the full path:

From Mac OS X El Capitan 2015 onwards (As of February 2018): Go to the folder of interest, right click on the folder, press the alt button + click on 'Copy "folder-name" as Pathname'. Go back to LipidQ and paste the folder path (⌘ Command button + V) into the output folder field.

Windows: Go to the folder of interest, right click on the folder, go to properties, find Location and copy the path there (Ctrl + C). Go back to LipidQ and paste the full path (Ctrl + V) into the output folder field. Remember to change every "\" in the path to "/".

3. Press 'Create column template file'

Finally the user specified column template names file is created by clicking on the 'Create column template file' button.

ELELAB/lipidQ documentation built on Feb. 24, 2020, 12:54 a.m.