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Table 3 Comparison with Conventional MS Methods

From: PEPPI: a peptidomic database of human protein isoforms for proteomics experiments

  MS with PEPPI 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