Group Resources:
RAId_DbS
is a software design to identify peptides in a
specified protein database using the information contained
in the MS/MS spectrum. One of the key features of
RAId_DbS
is that for each identified peptide it reports an
E-value based on a theoretical distribution
(
Alves
G., Ogurtsov Y.A., Yu Yi-Kuo. Biology Direct 2007, 2:25).
Another feature of
RAId_DbS
is that for each MS/MS
spectrum
RAId_DbS
reports a measure of goodness of its model.
RAId_DbS
has a unique database structure which incorporates
information from post-translational modifications (PTM),
single amino acid polymorphism (SAP) and diseases associated
with mutations (
Alves
G, Ogurtsov AY, Yu YK. BMC Genomics 2008, 9:505).
The information used to generated the
annotated database is obtained mainly from GeneBank.
Annotated databases from various species can be downloaded
from
https://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/RAId/RAId_Databases .
RAId_DbS's
unique database structure permits the user to
customize searches by including specific information
related to PTMs, SAPs and diseases by creating one's own
database which can be searched separately or together with
a specified database
(
Alves
G., Ogurtsov Y.A., Yu Yi-Kuo. arXiv:0803.2395).
RAId_aPS
is a new options available as part of
RAId.
RAId_aPS
can generate, for a given tandem mass spectrum,
the score distribution resulting from scoring all possible
peptides under a certain class of scoring functions. This
valuable information may aid development of a better measure
for assigning statistical significance to the peptide candidates.
Using a novel algorithm,
RAId_aPS
keeps track of the score
distribution together with the associated peptide lengths for
each score, providing proper score normalization
(
Alves
G., Ogurtsov Y.A., Yu Yi-Kuo. arXiv:0806.2685).
The current version of
RAId_aPS
allows the user to select from
four scoring functions to compute the "all possible peptides" score histogram:
RAId_DbS
scoring function
(
Alves
G., Ogurtsov Y.A., Yu Yi-Kuo. Biology Direct, 2:25), the second
scoring function is Kscore plugin
(
Mol Syst Biol. 2005;1:2005.0017.)
to X!Tandem, the third scoring function is X!Tandem hyperscore
(
Anal. Chem., 75, 768-774),
and the forth scoring function is the SEQUEST XCorr implementation by Crux
(
J Proteome Res. 2008 Jul;7(7):3022-7.).