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Table 1 Settings for protein profiling and data processing

From: Comparing the old and new generation SELDI-TOF MS: implications for serum protein profiling

  CRC sample set BC sample set
  PBS-IIc PCS 4000 PBS-IIc PCS 4000
SELDI analysis parameters
Samples CRC: n = 45
CON: n = 43
BC: n = 45
CON: n = 46
Array type CM10 IMAC30 Ni
Binding conditions 20 mM NaAc pH 5 PBS pH 7.4/0.5 M NaCl
Replicates 3 2
SELDI acquisition parameters
m/z range 0–200 kDa 0–200 kDa 0–200 kDa 0–200 kDa
Laser intensity 155 3500 nJ 155 3500 nJ
Detector sensitivity 6 n.a. 5 n.a
Deflector/detector attenuation 2000 Da 2000 Da 1000 Da 1000 Da
Laser shots kept 65 530 105 530
Not-assessable spectra CRC: 2/135
CON: 4/129
BC: 4/90
CON: 0/92
Cluster settings:     
First pass S/N 5 Valley depth 5 S/N 5 Valley depth 5
Second pass S/N 2 Valley depth 2 S/N 2 Valley depth 2
Cluster mass window 0.3% 0.3% 0.3% 0.3%
Present in 45% 45% 30% 30%
  1. n.a.: not applicable