JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy

Xusheng Wang,Yuxin Li,Zhiping Wu,Hong Wang,Haiyan Tan,Junmin Peng

doi:10.1074/mcp.o114.039586

Abstract

Database search programs are essential tools for identifying peptides via mass spectrometry (MS) in shotgun proteomics. Simultaneously achieving high sensitivity and high specificity during a database search is crucial for improving proteome coverage. Here we present JUMP, a new hybrid database search program that generates amino acid tags and ranks peptide spectrum matches (PSMs) by an integrated score from the tags and pattern matching. In a typical run of liquid chromatography coupled with high-resolution tandem MS, more than 95% of MS/MS spectra can generate at least one tag, whereas the remaining spectra are usually too poor to derive genuine PSMs. To enhance search sensitivity, the JUMP program enables the use of tags as short as one amino acid. Using a target-decoy strategy, we compared JUMP with other programs (e.g. SEQUEST, Mascot, PEAKS DB, and InsPecT) in the analysis of multiple datasets and found that JUMP outperformed these preexisting programs. JUMP also permitted the analysis of multiple co-fragmented peptides from "mixture spectra" to further increase PSMs. In addition, JUMP-derived tags allowed partial de novo sequencing and facilitated the unambiguous assignment of modified residues. In summary, JUMP is an effective database search algorithm complementary to current search programs.

Highlights

One common approach is to filter putative peptide spectrum matches (PSMs) to achieve a final list with a predefined false discovery rate (FDR) via a target-decoy strategy, in which decoy proteins are merged with target proteins in the same database for estimating false PSMs [23,24,25,26]
Evaluation of False Discovery Rate in JUMP via the TargetDecoy Strategy—JUMP is designed as a hybrid algorithm that performs de novo tag sequencing and matches tandem mass spectrometry (MS) spectra to a theoretical database (Fig. 1)
JUMP generated almost equal targets (n ϭ 6588) and decoys (n ϭ 6599) and similar distributions of PSM scores (i.e. J scores) in these targets and decoys. These results demonstrate that the target-decoy strategy is applicable for evaluating the FDR of JUMP-derived PSMs

Summary

Technological Innovation and Resources

JUMP: A Tag-based Database Search Tool for Peptide Identification with High Sensitivity and Accuracy*□S. Database search methods usually assign peptide sequences by comparing MS/MS spectra to theoretical peptide spectra predicted from a protein database, as exemplified in SEQUEST [9], Mascot [10], OMSSA [11], X!Tandem [12], Spectrum Mill [13], ProteinProspector [14], MyriMatch [15], Crux [16], MS-GFDB [17], Andromeda [18], BaMS2 [19], and Morpheus [20] Some other programs, such as SpectraST [21] and Pepitome [22], utilize a spectral library composed of experimentally identified and validated MS/MS spectra. It is a problem to set up an appropriate score threshold to achieve maximal sensitivity and high specificity [13, 27, 28]

JUMP Database Search Engine

EXPERIMENTAL PROCEDURES

RESULTS AND DISCUSSION

CONCLUSION