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Table 1 Summary of number of hits and processing time for each search engine (seconds to execute a search job using 1000 MS/MS spectra; note that many such jobs can be run in parallel)

From: APP: an Automated Proteomics Pipeline for the analysis of mass spectrometry data based on multiple open access tools

  X!Tandem: Native score X!Tandem: K-score Myrimatch
PSMs 3457 6166 6348
Peptides 1594 2357 2337
Average execution time (s) [distributed] 25 26 345
Average execution time (s) [single instance] 26 26 375
  MS-GF+ SpectraST Comet
PSMs 8655 1050 6155
Peptides 3407 578 2312
Average execution time - Distributed 3747 18 30
Average execution time - Single instance 4477 20 14
  All database search All DB Search and SpectraST  
PSMs 13029 13232  
Peptides 3505 3501  
  1. See Additional file 1: Figure S1 for an overview of the output provided by each search engine.