Table 2 Features used to encode a peptide sequence and its fragment ion sequences
From: MS2CNN: predicting MS/MS spectrum based on protein sequence using deep convolutional neural networks
Feature | Description | Package: function name |
|---|---|---|
m/z | Pyteomics v3.4.2: calculate_mass | |
 Original | m/z of the original sequence |  |
 Fragment ion | m/z of the fragment ion sequence |  |
Isoelectric point | isoelectric point of the sequence | Biopython 1.7: isoelectric_point |
Instability index | instability index of the sequence | Biopython 1.7: instability_index |
Aromaticity | aromaticity of the sequence | Biopython 1.7: aromaticity |
Secondary structure fraction | α-helix, β-strand and coil fraction of the sequence | Biopython 1.7: secondary_structure_fraction |
Helicity | helicity of the sequence | In-house program |
Hydrophobicity | hydrophobicity of the sequence | in-house program |
Basicity | basicity of the sequence | in-house program |