PEAKS
SPIDER Overview
SPIDER, Software Protein Identifier, is a sequence tag based search tool, which can be used to identify peptides that traditional tandem mass spectrometry ion search tools will miss. This is because it does not require an exact match to the spectrum, only similarly to the proposed sequence. PEAKS auto de novo sequencing is an ideal way to generate them.
If the protein we are analyzing is not in a database, SPIDER can identify peptides from the database that show significant homology to the de novo sequence. The ultimate need for this tool derives from using unsequenced organisms.
It should be emphasized here that BLAST IS NOT a peptide homology search tool. Many researchers have misunderstood that, resulting in, not just poor, but wrong data analysis. SPIDER is tolerant of common de novo sequencing errors such as (I/L), (N/GG) and (SAT/TAS). Thus it will not penalize the alignment if certain residues or combinations of the same mass are substituted, where as BLAST would fail here.
SPIDER can also be used to improve coverage on a protein that is already in a database, by seeking exact sequence matches and being plugged into a specialized database.
One cannot discuss this tool without mentioning speed. Click here to see a short video demonsration of SPIDER. Here we prove how fast it really runs, especially when using small data sets and small databases. It takes longer to say "SPIDER is very fast here," than to have a complete data set processed through a database. Other PEAKS Tutorials can be found here.
Relevant research papers and websites regarding SPIDER can be accessed here.
Y. Han, B. Ma, and K. Zhang: SPIDER: Software for Protein Identification from Sequence Tags Containing De Novo Sequencing Error. Journal of Bioinformatics and Computational Bioliogy 3(3):697-716. 2005.
I. Rogers: Assessment of an Amalgamative Approach to Protein Identification.
