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This report assesses the variation across fractionated sera processed over a one-month …

Biology Articles » Methods & Techniques » Laboratory methods to improve SELDI peak detection and quantitation » Tables

Tables
- Laboratory methods to improve SELDI peak detection and quantitation

Table 1
Fractions and ProteinChips considered having sufficient complexity for the analysis.
ProteinChip
 Fractions used in analysis
IMAC
 F1
 F3
 F4
F6
H50
 F1
 F3
 F4
F6
CM10-LS
 F1
 F3
 F4
 F5
 F6
CM10-HS
F3
 F4

Bold – denotes fractions to be highly variable across batches.
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 a
 No. Spectra excluded (Total 18)
 No. Peaks
 Averaged CV Peak Intensity (%)
 CV Range
 No. Peaks statistically (%) different across batches (p 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 b Analysis performed on 2 batches, not 3.
Table 3
Differences in sample processing and analysis setting between Exp.1 and Exp.2

EAM application
 Acquisition protocol optimization
 Specimen applied for optimization
 Spot correction
Exp.1
 Manual
 Chip specific
 Whole serum
 No
Exp.2
 Automated
 Chip and Fraction specific
 Appropriate serum fraction QC
 Yes

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