New Statistical Algorithms for the Analysis of Mass - FU Berlin, FB MI ...

66 CHAPTER 4. (BIO-)MEDICAL APPLICATIONS
combination of the three identified biomarkers (apolipoprotein A1, atrucated
form of transthyretin and a cleavage fragment of inter-alpha-trypsin
inhibitor heavy chain H4) is superior to CA-125 (cancer antigen 125, a
mucinous glycoprotein) alone in terms of sensitivity. CA-125 is a standard
tumor biomarker for ovarian cancer.
� (Honda et al., 2005) conducted a MS-based analysis of 245 plasma samples
from pancreatic cancer patients and controls. They found a fingerprint
(peak pattern) consisting of four peaks that was sufficient to
discriminate cancer patients from healthy subjects with a sensitivity of
91%. Combining this fingerprint with CA-19-9 (carbohydrate antigen
19-9) this sensitivity increased to 100%.
� (Hong et al., 2005) developed a MS-based approach for determining the
severity of multiple myeloma from serum of 64 newly diagnosed multiple
myeloma patients.
In addition to these reports excellent reviews are available, e.g. (Rosenblatt
et al., 2004; Thadikkaran et al., 2005; Omenn, 2006; Ebert et al., 2006).
The advantage of blood is that it has a very high protein concentration.
The bad news is, however, that only 22 proteins account for about 99% of
its protein content. These belong to the so-called high-abundance protein
species, including albumin (approximately 60% of the total protein in normal
human plasma), transferrins, immunoglobulins, etc. When interested in
low-abundance circulatory proteins, for example produced by tumors and especially
early-stage tumors, one must keep in mind that these will account
for less than 1% of the blood proteins. So, how to enrich the low-abundance
proteins become extraordinarily important in blood-based cancer proteomics
investigations.
As mentioned above, blood can be analyzed by two methods: (a) using the
plasma which is the liquid portion of blood in which the cells are suspended
or (b) using serum which is the fluid that remains after clotting proteins are
removed from plasma. Although, the advantage of using plasma is that it
contains more proteins and its protease activity is inhibited the same fact is
also a disadvantage: it is very difficult to detect low-abundance proteins in
the presence of many other (common, e.g. clotting) abundant proteins.
In principle, mass spectrometry-based proteomics analysis of blood can
be performed on both types, plasma and serum. However, there is still no
agreement in the community which is best:
� Regarding the ongoing enzymatic activity in serum (Koomen et al., 2005)
indicated that serum is not well suited for proteomics experiments because
even proteins that are not involved with the biologically relevant
pathways are cleaved as well by non specific proteases.
� (Tammen et al., 2005) recommended the use of platelet-depleted EDTA
or to citrate plasma for the analysis of the low-molecular-weight proteins.
� It was shown in (Villanueva, Shaffer, Philip, Chaparro, Erdjument-
Bromage, Olshen, Fleisher, Lilja, Brogi, Boyd, Sanchez-Carbayo, Holland,
Cordon-Cardo, Scher and Tempst, 2006) that - when focused on
analysis of low-molecular-weight proteome - serum is superior to plasma
as a source of diagnostic information in terms of peptidomics.
In this study, blood serum served as a basis for the acquisition of data.