The Arabidopsis Proteotypic Predictor (APP) takes a Arabidopsis Gene Initiative (AGI) identifier (eg At3g15020.1) or the amino acid sequence of an Arabidopsis protein, performs an in silico trypsin digestion and provides details of all resulting peptides, their mass, the number of potential miss cleavage sites, the presence and mass change of possible methionine oxidation, the proteins of the Arabidopsis proteome containing this peptide, the number of times a resulting peptide is present as a tryptic peptide in the Arabidopsis proteome and the probability of whether a peptide is predicted to be proteotypic based on the APP.
For an example please click the button at right to view the results for protein
a Sequences of characters 'ACDEFGHIKLMNPQRSTVWY' representing peptides.
Entering AGI identifiers
- The AGIs can be in the format of either At3g15020.1 or AT3G15020.1 and should be separated by spaces, TABs, commas or new-lines.
- If the program can't recognize if you have entered a list of AGIs then it will test if your input looks like a peptide sequence with any spaces, TABs or new-lines removed. In other words a "peptide sequence" is a sequence of "ACDEFGHIKLMNPQRSTVWY" characters with ignored spaces, TABs, and new-lines.
Entering peptide sequences
- Peptide sequences can be entered with with any spaces, TABs or new-lines included. APP will recognize "ACDEFGHIKLMNPQRSTVWY" characters and ignored spaces, TABs, and new-lines.
- Peptide sequences entered should be derived from TAIR10pep release.
Digestion Parameters
Digestion is carried out using Expasy Peptide Mass using trypsin as enzyme, maximum number of miss cleavages = 1, all cysteines in reduced form, variable methionine oxidation to form methionine sulfoxide. Monoisotopic masses of the occurring amino acid residues are used and peptide masses were recorded as [M+H]+. Resulting peptides out side of Mr of 500-3000 daltons are excluded.
Contact
Any questions or comments please email: nicolas.taylor [at] uwa.edu.au.
Probabilities
