Biology Reference
In-Depth Information
databases. Similar score schemes are exploited in MS-Fit,
27
Mascot,
28
and ProFound.
29
Complete reviews on these and other related scoring
functions are given in Refs.
30-33
Aldente
,
34
a PMF tool developed by the PIG and available from the
ExPASy server,
15
exploits the Hough transform to determine the mass
spectrometer deviation, to realign the experimental masses, and to
exclude outliers. This method is particularly insensitive to noise. Other
main features of Aldente are
•
a tuneable score parametrization, where the user can choose
the parameters that will be considered in the score and in what
proportion;
•
an extensive use of the UniProtKB/Swiss-Prot
35,36
annotations
such as protein mature form, PTMs, and alternative splicing, offering
a degree of protein characterization as part of the identification
procedure; and
•
the possibility for the user to define one or more chemical amino
acid modifications (besides the usual oxidation of methionine and
acrylamide adducts on cysteine residues, alkylation products on
cysteine residues, etc.), and to define the contributions of these
modifications to the score.
A stand-alone version of Aldente is commercialized as an in-house
solution.
b
3.2. PFF
PMF is an efficient approach when searching databases for species of
small and fully sequenced genomes. PFF is better adapted to searching
in larger databases as a more specific and sensitive identification
method when working with complex mixtures of peptides. Indeed, the
sequence information given by peptide fragmentation in MS/MS spec-
tra increases the chances of finding true positive hits in database
b
This version keeps track of the history of submitted jobs for easier job resubmission,
manages batch queries, and allows result annotation.
