Instead of defining study factors one the Study Definition page and assigning them to quan channels on the Sample page, you can create a study mapping file and import the study factors, the Quantification Method, and the associated quan channels when creating the new study.
TIP
The study definition file can be in Excel format or text format, but managing all the information in this file is easier when using Excel.
A study definition file is also useful when analyzing data downloaded from PRIDE or MassIVE. Projects in these repositories frequently include a text or Excel file that maps the quan channels to the study factors. This file might require only minor editing to be imported into a new study.
The following table describes the required columns for the study mapping file.
Column header | Content |
|---|---|
File | Full path to the raw data file, for example: C :\Data\TripleKnockout\TKOTT_1ms3_1.raw |
Quan Method (Reporter and Precursor Ion quan only) | The exact name of the Quantification Method in the Proteome Discoverer software (for example, TMT 11plex SG253828). If the name is not exactly correct, the study mapping file fails to import. Not included with label-free quantification data. |
Sample Type (Reporter and Precursor Ion quan only) | The options are either Sample Type or Control. The Control option is used in TMT experiments with multiple plexes that have a common control channel. |
Quan Channel | The individual quantification channel for multiplexed quantification methods. For TMT, an example is 127N reporter ion channel. For SILAC, an example is light, medium, or heavy. |
(Study factors) | There are three types of study factors:
Each factor has its own column with the format: Factor type: Factor name Here are examples for each factor type:
|
To see different example study definition files, see Triple Knockout TMT 11plex example.