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FindMod

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FindMod

FindMod is a tool that can predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides.

The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest [Documentation / Mass values and considered PTMs / References].

Run FindMod


1. Enter a sequence (mandatory):
Please enter one UniProtKB AC/ID (e.g. P20366 or TKN1_HUMAN). Alternatively, enter one protein sequence in single letter code.
Examples


If your submitted a sequence in one-letter code, please specify (if known) the source of your protein:
Eukaryote or Bacteria or Archaea or Virus ( Phage).

(This information will be used to determine whether certain post-translational modifications are likely to occur in your sequence.)

2. Enter a list of peptide masses (mandatory) and intensities (optional):
Enter a list of peptide masses and intensities that correspond to the specified protein. Enter one mass, space and its intensity per line:
Examples

Or upload a file from your computer, from which the peptide masses will be extracted (supported formats):


Check all or unmatching peptides for the following:
potential post-translational modifications (max. within one peptide).
Please note that if 3 is selected, then only a subset of modifications will be considered.
single amino acid substitutions.


3. Other PTMs to take into account (optional):
If you wish to take into account other PTMs than those already predictable by FindMod and FindPept tools, you can specify them here:

modification name amino acids
this modification
can be observed on 		atom composition
0 example ANF H: 3, O: 1, C: 2, N: , S:
1 H: , O: , C: , N: , S:
2 H: , O: , C: , N: , S:


4. Choose cysteine treatment (optional):
All peptide masses are with cysteines treated with:
with acrylamide adducts on cysteines
with methionines oxidized
with tryptophans oxidized
[M+H] + or [M] or [M-H] -
average or monoisotopic


5.Choose other parameters (optional):
Mass tolerance: ±
Select an enzyme :
Allow for missed cleavage sites (MC).

Display peptides sorted by peptide masses or in chronological order in the protein.


6. Send the results by e-mail (optional):
Your e-mail address:
Name of the unknown protein:


7. Submit or reset: