Table 1

Experimental conditions and statistics on database searches of four individual experiments using a single urine sample

In-gel 1

In-gel 2

In-solution 1

In-solution 2


Urinary protein

150 μg

150 μg

125 μg

125 μg

Albumin removal

-

-

+

+

Protein separation

Invitrogen NuPAGE 4-12% Bis-Tris 1D gel

Agilent mRP-C18 column

Number of fraction

14

10

22

22

Digestion

In-gel

In-gel

In-solution

In-solution

Denaturant

50% Trifluoroethanol

6 mol/l Urea + 2 mol/l thiourea

LC gradient time

100 min

140 min

100 min

100 min

Identified IT-MS2 spectra by Mascota

16,219

10,535

13,367

10,175

Number of unique peptidesa

4504

3853

3164

2637

Number of identified proteinsa

759

815

656

580

Total number of unique peptidesa

8041

Total number of identified proteinsa

1281


aApplied criteria are described in the Materials and methods section. 1D, one-dimensional; LC, liquid chromatography; MS, mass spectrometry.

Adachi et al. Genome Biology 2006 7:R80   doi:10.1186/gb-2006-7-9-r80

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