Table 3 Comparison with Conventional MS Methods

Sample

Same as right

Ordinary proteome samples

Spectrum

Same as right

Ordinary MS equipments

Software

Same as right

SEQUEST, Mascot, OMSSA etc.

Sequence Database

PEPPI or subset of PEPPI

Conventional protein sequence databases (IPI, UniProtKB, e.g.)

Detection Ability

1. Exonic region

2. Exon-Exon combinations (annotated transcripts)

3. Exon-Intron combinations

4. Intron-Exon combinations

5. Hypothetical Exon-Exon combinations

6. SNP peptides

Only proteins

Configuration

User configurable

Pre-defined by database producer

Cost

Same as right

Not very expensive