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Table 1 The parameters of database searching experiments

From: Speeding up tandem mass spectrometry-based database searching by longest common prefix

 

Instrument

LTQ

 

Spectra

107666 spectra extracted from ten raw files

Exp1

Database

18 purified proteins with the Uniprot/SwissProt protein sequence database(1020188 protein sequences, target + reversed), total around 460 MB

 

Digestion way

Site-specific digestion

 

Tolerance

Precursor: +/- 3Da; Fragment: +/- 0.5 Da

 

Modifications

Fixed: Carbamidomethylation (C) Variable: Oxidation (M)

 

Instrument

LTQ-FT or LTQ-Orbitrap

 

Spectra

13816 spectra extracted from two raw files

 

Database

IPI-Mouse protein sequence database(113914 protein sequences, target + reversed), total around 66 MB

Exp2

Digestion way

Non-specific digestion

 

Tolerance

Precursor: +/- 12 ppm; Fragment: +/- 0.5 Da

 

Modifications

Fixed: Carbamidomethylation (C) Variable: Phosphorylation (S, T, Y) Oxidation (M),