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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.