Speeding up tandem mass spectrometry-based database searching by longest common prefix.
BACKGROUND
Tandem mass spectrometry-based database searching has become an important technology for peptide and protein identification. One of the key challenges in database searching is the remarkable increase in computational demand, brought about by the expansion of protein databases, semi- or non-specific enzymatic digestion, post-translational modifications and other factors. Some software tools choose peptide indexing to accelerate processing. However, peptide indexing requires a large amount of time and space for construction, especially for the non-specific digestion. Additionally, it is not flexible to use.


RESULTS
We developed an algorithm based on the longest common prefix (ABLCP) to efficiently organize a protein sequence database. The longest common prefix is a data structure that is always coupled to the suffix array. It eliminates redundant candidate peptides in databases and reduces the corresponding peptide-spectrum matching times, thereby decreasing the identification time. This algorithm is based on the property of the longest common prefix. Even enzymatic digestion poses a challenge to this property, but some adjustments can be made to this algorithm to ensure that no candidate peptides are omitted. Compared with peptide indexing, ABLCP requires much less time and space for construction and is subject to fewer restrictions.


CONCLUSIONS
The ABLCP algorithm can help to improve data analysis efficiency. A software tool implementing this algorithm is available at http://pfind.ict.ac.cn/pfind2dot5/index.htm.
Key Lab of Intelligent Information Processing, Chinese Academy of Sciences, Beijing 100190, China.
Chen
C
Zhou
Hao
H
Chi
Le-Heng
LH
Wang
You
Y
Li
Yan-Jie
YJ
Wu
Yan
Y
Fu
Rui-Xiang
RX
Sun
Si-Min
SM
He
D000465:Algorithms; D030562:Databases, Protein; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010455:Peptides; D011506:Proteins