ProteinCenter User Manual
Table of Contents

Chapter 12. Peptides view

Table of Contents

12.1. The peptides view

12.1. The peptides view

The peptides view shows each unique peptide in a dataset. This means that even if the same peptide has been identified for several accession keys (proteins) in the dataset, it is listed only once.

Figure 12.1. Peptides view

Peptides view

Below is a short description of the most common columns in the peptides view. To manually select which columns to display, see Section 5.4.5, “Selecting which columns to display”.

  1. Exp. data - The number of experimental data where this peptide exists. This is a link that, when clicked, displays a sub-table containing those data.

  2. Peptide - the peptide sequence. Modified amino acids are displayed in red. N- and c-terminal modifications are shown in red on appended lower-case 'n' and 'c' residues.

  3. Modification - if any amino acids are modified, the name of their modifications are displayed here. Modifications not recognized at import time as a standard UniMod modification, are characterized as 'Unknown'.

  4. Position - if any amino acids are modified, the position of the modifications are displayed here. N- and c-terminal modifications are given at positions zero and one beyond sequence length.

  5. AA - if any amino acids are modified, their short names are displayed here. N- and c-terminal modifications are shown as short names 'N-t' and 'C-t'.

  6. Observed - if any amino acids are modified, their observed masses are displayed here.

  7. Mono. mass - if any amino acids are modified, their monoisotopic masses are displayed here.

  8. Avg. mass - if any amino acids are modified, their average masses are displayed here.

  9. IPP - initial peptide probability

  10. pI - The predicted isoelectric point of the peptide, based on the sequence only (post-translational modifications are not taken into consideration).

  11. GRAVY - Grand average of hydropathy, i.e. the sum of hydropathy values of all the amino acids in the sequence, divided by the number of residues.

Other columns can be shown also, depending on the type of data. For example, Mascot files may contain iTRAQ quantitation on the peptide level.

Like the other list views, the functions described below exists for selecting, deleting and saving data.

Figure 12.2. Data handling functions

Data handling functions

Looking at the above figure, the functions from left to right are:

  • Save selected data as a new dataset.

  • Delete selected data from the current dataset.

  • Select all data that is not removed by any applied filters. Peptides cannot be selected individually, so it is actually the owning experimental data that is selected.

  • Removes all selections including selections on data not removed by applied filters.