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Experimental Design
The purpose of specifying the experimental design is to provide FlashLFQ with extra information about the spectra files you want to search; specifically each file's condition (e.g., normal or cancer tissue), the sample number, the fraction (if your samples are fractionated), and the replicate number. This information is used to normalize intensities, perform statistical analysis, and improve match-between-runs.
Requirements for each designation for experimental design are listed here:
- Condition - Cannot be blank
- Sample - an integer, at least 1. Each condition must have continuous sample numbers starting at 1. For example, samples 1, 3, and 4 are not valid because sample 2 is missing. In this case you would label the samples as 1, 2, and 3.
- Fraction - an integer, at least 1. Each sample must have continuous fraction numbers starting at 1. If your data is not fractionated, just enter 1 for all fractions. It is OK for two samples to have different total numbers of fractions. It is NOT recommended to use a sample if it is missing a fraction with significant peptide intensity (e.g., if sample 2 is missing fraction #5 out of 10 total fractions).
- Replicate - an integer, at least 1. Each fraction must have continuous replicate numbers starting at 1.
The experimental design is saved to a file called ExperimentalDesign.tsv. There is no practical reason why you would want to alter this file manually if you are using the GUI (graphical user interface). If you are using the command-line version, however, you will need to create the .tsv file yourself manually. An example file is attached on the bottom of this page. Be sure to follow the formatting rules above.
Note: You do not need to download this if you're using the graphical version of FlashLFQ. You only need to download this and edit it manually if you're running the command-line version of FlashLFQ.