Table 2

Summary table of results comparing Exp.1 and Exp.2 showing improvement in peak detection and peak intensity variation following optimization of protocols.


Experiment 1
 Experiment 2


Protein Chip
 Fraction
 No. Spectra excluded (Total 18)
 No. Peaks
 Averaged CV Peak Intensity (%)
 CV Range
 No. Peaks (%) statistically different across batches (p < 0.01)a
 No. Spectra excluded (Total 18)
 No. Peaks
 Averaged CV Peak Intensity (%)
 CV Range
 No. Peaks statistically (%) different across batches (p < 0.01)a

F1
 5
 16
 31.7
 12–127
 0
 1
 28
 20.9
 8–36
 2 (7)

F3
 1
 11
 31.2
 15–75
 0
 0
 21
 31.4
 12–52
 2 (10)
IMAC
 F4
 3
 7
 44.7
 29–61
 1 (14)
 0
 20
 26.0
 14–45
 2 (10)

F6
 3
 21
 27.0
 15–39
 0
 7
 27
 22.6
 11–49
 9 (33)

LS-F1
 4
 22
 31.0
 15–50
 0
 1
 23
 18.1
 11–41
 1 (4)

LS-F3
 6
 5
 41.5
 25–48
 0
 0
 23
 26.4
 13–40
 3 (13)

LS-F4
 1
 13
 37.4
 18–55
 6 (46)
 1
 26
 14.7
 8–30
 0
CM10
 LS-F5
 4
 9
 30.6
 20–46
 3 (33)
 0
 27
 16.4
 8–30
 1 (4)

LS-F6
 3
 13
 29.4
 18–44
 0
 2
 30
 25.4
 8–50
 11 (37)

HS-F3
 6
 3
 66.5
 53–85
 0b
 1
 15
 49.2
 27–148
 9 (60)

HS-F4
 6
 5
 48.7
 19–72
 0
 3
 14
 30.6
 10–46
 0

F1
 5
 6
 67.5
 40–129
 0
 0
 16
 32.7
 15–66
 2 (13)

F3
 0
 13
 32.4
 16–50
 3 (23)
 1
 17
 22.8
 15–38
 5 (29)
H50
 F4
 2
 15
 33.0
 15–79
 2 (15)
 1
 21
 22.5
 11–53
 5 (24)

F6
 2
 30
 23.7
 13–39
 1 (3)
 1
 35
 25.0
 12–55
 3 (9)

a This column reports the number of peaks in the ProteinChip-fraction spectra that were considered to have different peak intensities between batches as calculated by the non-parametric Kruskal-Wallis (p < 0.01), the data was bootstrapped using 2000 randomizations of the experiments to correct for multiple testing.

b Analysis performed on 2 batches, not 3.

Rollin et al. Proteome Science 2007 5:9   doi:10.1186/1477-5956-5-9