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 these sequences.
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 SPIDER derives from using unsequenced organisms.
It should be emphasized 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 SPIDER 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.
To learn more about how SPIDER works to optimize sequences, click onto our Sequence Tag Homology page. This page explains the 3 sequence tag homology methods (Segment Match, Non-Gapped Homology Match and Homology Match) utilized in SPIDER, as well as how to interpret the results.
