1. Introduction

JUMP SYSTEM is a software integrating database creation, database search, identification filtering and protein quantification. The system starts with a raw file and ends with a list protein of interest. It is capable of identifying multiple candidate peptides from mixture spectra and producing de novo sequence tags and generates a Jscore that merges the local tag score and the global pattern matching score. JUMP is a sensitive and specific database search method for peptide identification and outperforms than other search engines such as SEQUEST, Mascot, InsPecT, and PEAKS DB. Currently, JUMP SYSTEM has four main components: database creation, database search, identification filtering, and protein quantification.

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