FIGURES AND TABLES

Figure 1.

Experimental set-up. Two separate samples sets were analysed according to two previously published methods. In addition, a modified version of one of the methods was used to yield better peaks (see Results section).

Figure 2.

Spectra parts generated according to Tolson's procedure. (a) Samples from set 1 and set 2 are shown. The 11-kDa peaks are visible in a subset of the RCC sera (arrow), but not in those from HC. (b) Comparison of one of our spectra with the one reported by Tolson et al. Nearly all peaks present in the Tolson spectrum were visible in our spectrum (arrows), although some with lower peak intensities, which is possibly due to the fact that the published spectrum was acquired with extra high laser intensity for peaks >10 kDa. Tolson spectrum reprinted by permission from Macmillan Publishers Ltd: [Lab Invest],⁸ copyright 2004.

Figure 3.

Detection of the 11-kDa cluster in healthy controls (HC) from sample sets 1 and 2. The straight line represents the noise level.

Figure 4.

Optimisation of SELDI-TOF MS acquisition parameters for detection of the Won peaks (1–5). Two RCC samples were used for optimisation (A and B). Both laser intensity and detector sensitivity were optimised separately.

Figure 5.

Classification tree reported by Won et al. The primary node includes the peak at 4107lDa, which roughly separates between patients (left branch) and controls (right branch). Reprinted with permission from Wiley-VCH verlag GmbH & Co KG.

Figure 6.

Spectra parts generated with Won's original procedure (a) and with a slightly modified one (b). The same samples in set 1 and set 2 are shown for either assay. Peak intensities for the peaks of interest at 3901, 4107, 4153, 5352 and 5987 Da (peaks 1–5) are higher in the modified procedure.

Figure 7.

Identification of the serum amyloid- (SAA) peak cluster by immunocapture. The spectra parts successively show protein profiling on NP20 chip of the serum fraction that has not bound to the SAA-1 antibody, the fraction that has bound to this antibody on NP20 chip and on CM10 chip, the unbound serum fraction on CM10 chip and the original protein profile of whole serum on CM10 chip. Peaks 1–3 represent des-RS SAA-1 (11.4 kDa), des-R SAA-1 (11.5 kDa) and SAA-1 (11.68 kDa), respectively. The peak at 11.9 kDa (4) may be another post-translationally modified form of SAA-1. The fifth peak at 10.8 kDa may be the same as found by Tolson, although it was not reported to be a form of SAA-1.

Figure 8.

Correlation of serum levels of SAA as measured by ELISA with peak intensities of the 11.68-kDa peak from SELDI-TOF MS protein profiling.

Table 1 - Patient and sample characteristics of sample sets 1 and 2 compared to those of Won and Tolson.

Table 2 - Comparison of peak detection in Tolson's samples and in our sets 1 and 2.

Table 3 - Abundances of Tolson peaks (peak height 'averages' of duplicate analysis and concentrations measured by ELISA) and patient characteristics.

Table 4 - Spectra from the Won method included for data analysis.