PTM Proteomics - Differential Analysis

The input form for differential analysis file requires a tabulated text file with at least 9 columns with the following example.

Different to the total proteomics differential analysis file, a separate UniProt Accession ID column is required since the primary id.

• In the example image above, the Index column contains the primary id and was assigned as the Select Primary IDs parameter.

• For Select UniProt Accession IsD parameter, the ProteinID column was assigned which contains the acc id, including isoform information.

• The Select Probability Score parameter was assigned the MaxPepProb column which contains the probability score given to the PTM site should only contain 1 single value.

• The Select Fold Change parameter was assigned the Welch's T-test Difference AO_UT column (Log2 Fold Change column) and Select Significant parameter was assigned the -Log Welch's T-test p-value AO_UT column (-Log10 Significance column).

• The Sequence Window parameter was assigned the SequenceWindow column should only contain 1 value.

• The Peptide sequences parameter was assigned the Peptide column should only contain 1 value.

• The PTM positions parameter was assigned the Positions column with the position of the PTM within the protein sequence; should only contain 1 value.

• The PTM positions in peptides parameter was assigned the Position.in.peptide column with the position of the PTM within the peptide sequence; should only contain 1 value.

An aspect similar to the total proteomics differential analysis file is the Comparison parameter. If your data is in long form format where there is a column which indicates the label of the different comparisons, you can assign Comparison parameter as that column. After that, you can select the label of the comparison of interests from the Select Comparison parameter. By default, if these two parameters are not assigned, Curtain will automatically give Comparison parameter CurtainSetComparison column name and Select Comparison parameter the value 1.

If your fold change data and/or significannce data are not appropriately log transformed, you can tick the appropriate check box underneath each parameter to have curtain perform log transformation.