Introduction
Peptide mass fingerprinting involves the digestion of an unknown protein with a proteinase of known cleavage specificity and the measurement of the resulting peptides by mass spectrometry.
Those experimentally measured peptide masses are then compared with the theoretical peptides calculated for all proteins in a protein sequence database.
One of the main ideas of Aldente is to avoid calibration problems by
taking into account the mass spectrometer deviation.
It implements a number of rules, empirical observations and user
knowledge that approach the expert human interpretation of results in
various steps of the identification procedure.
The procedure can be divided into 3 steps:
- The selection of experimental MS peaks to be matched with
theoretical peptide masses within a user defined tolerance space.
- The interpretation of the experimental calibration deviation of
the instrument: exclusion of false matches and reduction of the
tolerance space to the internal deviation of the instrument.
- The entirely tuneable scoring and ranking system
of the protein entries that allow correct interpretation of real
identifications, presence of protein mixtures, etc.
Aldente proposes a realignment of experimental masses using the Hough
tranform. The Hough Transform is standard method
used in image analysis for finding straight lines hidden in larger amounts
of other data.
It is a robust method, therefore not sensitive to noise. It has no
difficulties to work with very crowded spectra (i.e. with a lot of
input masses, more then 100) and with a lot of theoretical masses (that
can be generated when considering the combinatory related with
heterogeneously modified or missed-cleaved peptides).
The output provides a significant amount of useful information. It
includes identified proteins and peptides, as well as the
deviation function used, and the worked out ambiguities. Links to
ExPASy characterization tools (currently FindMod, GlycoMod, FindPept) are also provided.
For information about the Hough transform you may go to the following URLs: