Table 1 Settings for protein profiling and data processing
From: Comparing the old and new generation SELDI-TOF MS: implications for serum protein profiling
| Â | CRC sample set | BC sample set | ||
|---|---|---|---|---|
| Â | 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: | Â | Â | Â | Â |
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% |