Biology Reference
In-Depth Information
between experimental spectra and sequence entries of a database; but in
contrast to classical search tools, they implement algorithms optimized
to match spectra with unexpected mass shifts such as PTMs and/or
transpeptidations. Four programs are known to a large community:
GutenTag,
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Modiro,
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Popitam,
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and InsPecT.
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Open modification
search algorithms are designed to take into account any type of modifi-
cation that would allow a better match between the spectrum peak pat-
tern and a candidate peptide.
Popitam was developed by the PIG. Original features of Popitam are
(a) the sequence-guided tag extraction performed by the simultaneous
parsing of the spectrum graph and of an indexed representation of a can-
didate sequence; and (b) the tag compatibility graph, in which cliques
represent possible interpretation scenarios of the spectrum; and (c) opti-
mization of scoring functions using parallel multi-objective genetic program-
ming. Popitam is specially adapted to deal with PTMs, mutations, missed
cleavages or half-cleavages, and transpeptidation. This list can be extended
to other events, like errors in databases, badly calibrated data or imprecise
precursor masses, and in general any event that modifies the sequence or
residue masses of a peptide analyzed by MS. Popitam is currently available
on the ExPASy server (http://www.expasy.org/tools/popitam/).
3.3. Identification Platforms — SwissPIT
Software tools are run several times in order to empirically discover the
best parameter settings.
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When various strategies of MS analysis are
used, the results are manually selected and combined. In most situa-
tions, though, only one single tool is utilized for protein identification
along with a unique parameter setting. Many spectra are thus missed
due to inappropriate parameter values, to inadequate filtering, or merely
to underperformance of certain scoring schemes for the quality of the
spectra at hand. The flexible automation of computer tasks as well as a
combination of different workflow strategies are thus necessary to
enhance data analysis, to reduce human interaction, and to achieve
high-throughput analysis. Therefore, a major goal in MS/MS identifi-
cation projects is the matching of as many spectra as possible while keep-
ing the false-positive rate as low as possible. The most promising way to
