PepID – Rapid identification of peptide sequences based on amino acid composition

The function of the PepID tool is to demonstrate the implementation of the algorithm developed for the identification of peptides based on their composition that has been developed as part of the MCW NHLBI Proteomics Center project. This algorithm uses clustering techniques derived from data mining to generate a hierarchical index of peptide amino acid attribute (PAA) vectors. A query peptide composition derived from sequence or MS data is used as to identify the matching peptide in the database using an indexed lookup. This method is much less computationally intensive and therefore potentially faster than the pair-wise methods of peptide identification currently used.

ProMoST – High precision mass and pK calculations for native and modified proteins

Biologically, protein modifications are one of the most important regulators protein function. It has been long known that many protein modifications lead to a change in mass, and more importantly, a change in the charge of the protein. These changes can be readily observed using 2 dimensional gel electrophoresis. ProMoST allows for the calculation of high precision values for the molecular mass and predicted pI for unmodified proteins and proteins with predefined or user defined modifications. ProMoST allows the user to alter the pK values used for the pI calculation and new modifications can be defined. The results can be output as a text file or an Excel .xls file and/or visualized as a table of calculated values or a graphic representation of a theoretical 2D gel.