performance of protein microarrays using SEREX derived antigens paper

2014-08-29

azim58 - performance of protein microarrays using SEREX derived antigens
paper

paper found here
C:\kurt\storage\CIM Research Folder\DR\2012\12-14-12\serex paper
and here
paper found here: "C:\kurt\storage\CIM Research
Folder\DR\2013\1-26-13\some_serex_papers\Tumour auto-antibody screening
performance of protein microarrays using SEREX derived antigens.pdf"
PMID: 21078204

first started reading 12-14-12

notes
Tumour auto-antibody screening: performance of protein microarrays using
SEREX derived antigens
BMC Cancer 2010
from Austrian Institute of Technology

people often do gene expression profiling

they make protein microarrays. However, the proteins included on their
array are derived from the standard SEREX approach where clones are lysed
directly on the membrane and working with the large membranes is a
cumbersome process.

They produced his tagged protiens

they detected high levels of antibodies against e coli proteins in the
sera of all donors and patients

they had better detection limit/signal intensity with the microarray than
the macroarray

they used the limma R software package

they had good correlation between samples

they could distinguish between brain and lung cancer sera samples based
on their reactivity for certain clones

SEREX arrays for screening several thousand expression clones

q
Drawbacks of
membrane based screening are low reproducibility, low
dynamic range of signal intensities, and difficulties in
handling membranes.

q
We have found
during optimization (data not shown) of protein microarray
production that proteins concentrations of up to
0.5 mg/mL are well suited for spotting using a contact spotter.

they could screen 20000 different spots on the microarray

? I wonder why they didn't compare cancer with normal as well. Instead,
they compared lung cancer with brain cancer.

===========================================================================
notes from when I accidentally started reading the paper a 2nd time
1-27-13

microarrays have advantages over macroarrays

q
Mutated, modified and aberrantly expressed proteins
evoke an immunological response leading to the
production of auto-antibodies [5,6].

q
However, protein microarrays have great
potential to characterize auto-antibodies [9].

q
Over recent years most approaches have used so called
macroarrays for autoantigen-profiling.

q
Handling membranes and processing
sera is cumbersome, and sensitivity and reproducibility of
these macroarrays are limiting.

q
16 bit
(0-216) dynamic range of standard microarrays.

q
The bacterial wet biomass (30 mg/mL culture) obtained by
autoinduction was twice when compared to that of
obtained from IPTG cultures.

q
Positive control spots of E. coli crude protein
extracts showed high signals indicating the presence
of high levels of antibodies against E. coli proteins in the
sera of all donors and patients, whereas buffer spots serve
as controls were clearly negative.

q
This might be due to the smaller reaction surfaces and
better distribution of the serum-sample over the array
(Figure 1)

^explaining why the microarray gave a greater detection limit/signal
intensity than the macroarray

high reproducibility
q
correlation
coefficients ranging from 0.92 to 0.96

azim58wiki: