What it does

Protein summarisation and label free quantitation.

Inputs

• Quantification input: Tabular file with the summary output from moFF or in case other tools were used for peptide quantitation with the following columns: 'peptides' containing the amino acid sequence; 'prot' with the Uniprot Accession and then one column per sample with the quantitation values.

  peptides     prot       sample1    sample2
  AAABDEK      B9DM54     1809446    563862
  TELATASDR    Q9CFE8     294282     457023
  AMGLATK      P85660     194023     428277
    ...
    ...
  

• Metadata input: Separate columns with sample names, condition and optionally also lab and machine. Sample names must match exactly the sample names from the peptide quantitation columns in the previous tabular file.

  sample     condition
  sample1    healthy
  sample2    disease
    ...
    ...
  

Options

• Summarisation only: Summarisation is done through robust regression to take also the peptide effect into account. In case only sample column is provided median protein intensity is calculated.
• Summarisation and quantification: Relative quantification is performed according to the information provided in the metadata file.

Outputs

• Summarised protein output: Uniprot accession and quantitation values per sample and protein
• Quantification output: Uniprot accession, comparison between conditions, fold change, p-value, q-value