Input Data Format

This page details the required format for the input data used in this R package. The package requires one primary data file (for protein/analyte values) and can optionally accept a second file containing experimental conditions or sample metadata.

1. Protein Data File

The main input is a dataframe containing your protein expression data. The structure must follow these rules:

• Rows: Each row should represent a single protein or analyte.
• Columns: The columns should contain both metadata about the proteins (e.g., Protein ID, Gene Name, UniProt Accession) and the quantitative values for each sample. The column headers for your samples will be used to link to the condition data. Sample columns must come after analyte metadata columns.

Example Protein Data Table

Here is a small example of a correctly formatted protein data dataframe. Columns ProteinID and Gene.Name are metadata, while Sample_A, Sample_B, Sample_C, and Sample_D contain the measurements for each sample.

ProteinID	Gene.Name	Description	Sample_A	Sample_B	Sample_C	Sample_D
P12345	GENEA	Protein A Description	1.2	1.5	5.5	5.9
P67890	GENEB	Protein B Description	2.5	2.8	6.2	6.5
Q54321	GENEC	Protein C Description	3.1	3.3	7.8	7.5
Q09876	GENED	Protein D Description	4.0	4.2	8.1	8.3

Example Protein Data Structure

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2. Condition Metadata File (Optional)

You can provide an optional second dataframe that describes the experimental conditions for each sample. This file is highly recommended for downstream analysis.

• Crucial Requirement: This dataframe MUST contain a column named SampleID.
• The values in the SampleID column MUST exactly match the column names of the samples in your protein data file (e.g., Sample_A, Sample_B, etc.). Rows with SampleIDs missing from the data will be dropped. If SampleIDs are missing in the condition file, a new row with all NA entries will be added.
• Other columns can contain any metadata you wish to associate with your samples, such as treatment group, time point, batch, etc.

Example Condition Data Table

This is an example of a correctly formatted condition dataframe that corresponds to the protein data example above.

SampleID	Condition	Timepoint	Batch
Sample_A	Control	24h	1
Sample_B	Control	24h	1
Sample_C	Treated	24h	2
Sample_D	Treated	24h	2

Example Condition/Metadata Structure

Important: A mismatch in sample names between the protein data columns and the SampleID column in the condition file will result in dropped rows or the addition of empty rows. Please ensure they are identical.