P-Mod and SALSA Data Analysis Software
Our laboratory has developed to novel data analysis tools,
P-Mod and SALSA. Both applications
are used to search MS-MS data to detect spectra that encode peptides
or chemical species of interest. These programs do not search
databases. Instead, they search datafiles to identify spectra
that match user-specified characteristics (SALSA) or correspond
to peptide search sequences and their modified forms (P-Mod).
One would use SALSA or P-Mod when you know, either because of
the nature of the sample analyzed or from the result of a database
search (e.g. Sequest) that a particular protein is represented
in the dataset. However, other spectra not matched by Sequest
to those proteins may correspond to modified forms. You would
use SALSA or P-Mod to search for additional spectra that correspond
to these modified or variant forms of the protein(s) of interest.
If you want to quickly determine whether the dataset contains
spectra that encode modified peptide forms, P-Mod is the best
tool to use. P-Mod searches the peptides from the protein sequence
of interest against the dataset. P-Mod looks for mass differences
between the peptide search sequence and the precursor of each
MS-MS spectrum and then identifies the best sequence-to-spectrum
matches, the masses of the modifications and their sequence positions.
P-Mod also calculates a p-value to indicate the probability that
the reported matches are nonrandom.
SALSA is a more generic data analysis tool that can be applied
to any MS data. SALSA allows the user to specify combinations
of spectral features, including product ions, losses, ion pairs
and series and generate custom searches that identify spectra
containing these features. The user then must inspect the spectra
manually to determine what information is encoded in the spectrum.
SALSA scores do not indicate statistical probabilities and merely
rank spectra based on their correspondence to the search criteria.
SALSA searches with ion series corresponding to peptide sequence
motifs can identify spectra of both unmodified and modified sequences,
but the process of identifying modifications in an entire protein
sequence is much slower than with P-Mod. Nevertheless, because
SALSA can score features that P-Mod cannot (e.g., loss ions and
user-designated product ions), SALSA is the ultimate customizable
MS data search tool.
Both P-Mod and SALSA complement database search tools, such as
Sequest, Mascot and X!Tandem because they can identify MS-MS spectra
corresponding to modified or variant forms of proteins and peptides.
Because both programs search for spectra displaying characteristics
of user-specified protein and peptide sequences, they can detect
spectra of both unmodified and modified peptides, even if the
mass and amino acid specificity of the modification cannot be
specified beforehand.
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