MS²PIP takes a PEPREC (Peptide Record) file as an input. This is a space-separated file that lists all peptides. To run our server smoothly, we limit the number of peptides to 10 000. If you need to predict more peptide spectra, we recommend you to split-up your dataset into multiple batches, or to download MS²PIP from GitHub and run it locally.
A PEPREC file contains the following columns:
spec_id: A unique ID for the peptide.
peptide: Peptide sequence.
modifications: PTMs for the given peptide. Every modification is listed as
name|location, separated by a pipe (
|) between the name, the location and other PTMs. The location is an integer counted starting at
1for the first AA.
0is reserved for N-terminal modifications.
Namehas to correspond to a preset or custom PTM (see below) . Unmodified peptides are marked with a hyphen (
charge: Precursor charge of the peptide.
Example of a PEPREC file:
spec_id modifications peptide charge
peptide1 - ACDE 2
peptide2 2|Carbamidomethyl ACDEFGHI 3
peptide3 0|iTRAQ|10|Oxidation ACDEFGHIKMNPQ 2
A list of all modifications and the corresponding mass shifts is needed for MS²PIP to properly calculate the fragmentation peak m/z values. You can select some preset modifications below or provide your own list. For the preset modifications, we use the PSI-MS names and monoisotopic mass shifts from Unimod. This means that, if you use these preset modifications, the modification names in your PEPREC file need to match the Unimod PSI-MS names. If MS²PIP encounters a modification in the PEPREC file that is not provided in the modifications list, it will skip that peptide.
If you provide your own list of modifications, each line can only contain one modification, with the following comma-separated properties:
If a certain modification occurs on different amino acids, every modification-amino acid combination
should have it's own entry and have a unique name
N- and C-terminal modifications can be added in the same way, but require
C-term instead of an amino acid code.
Example a of custom modification list: