Customer Newsletter September 2008 Contents • New Aminosilane Slide • Protein Microarrays • Antibody arrays • News and Exhibition calendar

1. Microarray Solutions
Edition # 4 / September 2008
The Nexterion® Newsletter
Editorial.........................................................2
New Aminosilane Slide.................................3
Nexterion® Slide AStar
Protein Microarrays....................................4-5
Selecting the optimal surface for your protein
microarray
Antibody Arrays.............................................6
Epitome Biosystems, Boston, MA: Ti-Tyr™
Profiling chips for detection and quantification of
phosphorylation sites
News.............................................................7
Latest news from SCHOTT
Meet us.........................................................8
Conference and exhibition calendar
Competition...................................................8
Win an iPod
The Nexterion® Newsletter © SCHOTT

2. The Nexterion® Newsletter #4 September 2008 page 2
2
Editorial
Dear Reader,
Welcome to the latest edition of the SCHOTT “Microarray Solutions”
newsletter. Since the last edition, there have been a number of developments
at SCHOTT that we hope will continue to allow us to offer the latest microarray
substrates and accessories. Some of these developments will be covered in
this newsletter, including the launch of a new coated slide product, and
SCHOTT’s continued focus on developing the best range of slide surfaces for
protein microarrays.
When SCHOTT first entered the microarray slide business back in 2002,
Christian Jabschinsky aminosilane coated substrates were by far the most popular choice for printing
General Manager PCR products. Even after all this time, aminosilane still remains an extremely
Nexterion – Microarray popular slide surface for printing DNA microarrays. As a result of this
Solutions continued popularity, SCHOTT will soon launch what we feel will be the best
aminosilane coated substrate in the market, Nexterion® Slide AStar. There is a
short interview with Dr Dietrich in this newsletter that gives some insights into
the background and development of the product.
Last year, SCHOTT introduced a range of new Nitrocellulose slides
(Nexterion® Slide NC). These were jointly developed by SCHOTT and
Sartorius Stedim to address the needs of the rapidly growing protein
microarray market. The high level of customer interest in Nexterion® Slide NC,
and other SCHOTT surfaces, led to our decision to give a presentation on
“How to select the most appropriate protein microarray surface” at PepTalk
2008 in San Diego, CA. The talk was well received both by the delegates and
the press. In this issue we look back on Dr. Dietmar Knoll’s talk, and hopefully
offer some invaluable advice on key factors to consider when selecting the
most appropriate slide surface.
This edition of “Microarray Solutions” will also introduce you to our exciting
new product catalogue, and the newly developed web based “Frequently
Asked Questions”. These will both help to complement the first class technical
and customer support SCHOTT continues to strive to offer all our customers.
I hope that you will enjoy reading this edition of our newsletter and, as always,
please feel free to contact us if you have any ideas for articles you would like
to see in future editions. These could include having your facility and research
work with Nexterion® product featured, or a suggestion for an application area
that you would like us to focus on. Finally don’t forget to enter our competition
to win an iPod Classic. Viel Glück!
Regards,
Christian Jabschinsky
© SCHOTT

3. The Nexterion® Newsletter #4 September 2008 page 3
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NEW Nexterion® Slide AStar
Taking Aminosilane Slide Performance to the Next
Level
In this article we discuss the development of the new aminosilane slide from
SCHOTT with the Director of R&D, Dr. Rüdiger Dietrich.
MS: Why did SCHOTT decide to develop yet another Aminosilane coated
slide?
RD: That’s a good question! Aminosilane slides still remain the most popular
choice for printing both PCR products, and longer oligonucleotides. This is
despite the widespread availability of potentially superior surface chemistries.
To better address the needs of the current market, and in collaboration with
colleagues in marketing, we developed a specification for a new “high
performance” aminosilane slide (see table on left).
MS: What were seen as important parameters for the new slide?
Specification for AStar Coating RD: We agreed targets for performance characteristics such as a spot size
with typical spotting buffer and conditions, required shelf lives of unprinted
• Contact angle 50° and printed slides, low background and high coating uniformity. Developing a
• Target spot size 100 microns commercial product is always a balance between creating the best product
• Low fluorescence background technically, and practical considerations like; are the reagents that we want to
(allowing long term storage of use readily availability for at least two suppliers at a reasonable cost? From
printed slide) the production point of view, a major consideration was that the slides must be
• Distinguished coating able to be produced in a robust and stable process. Fortunately the seven
uniformity, CV’s < 5% years experience SCHOTT has with slide coating technologies was a major
• Robust and stable (highly advantage in this respect. Alongside optimising the production process we
reproducible) coating process have also developed new quality control for checking things like coating
• Economic production costs homogeneity.
MS: SCHOTT already offers two aminosilane coated slides, isn’t adding
a third going to confuse customers?
RD: Yes, potentially this could be a problem, and for this reason we have
decided, in future, just to offer two type of aminosilane slides, Nexterion ® Slide
A+, and Slide AStar. The current Nexterion® Slide A will still be available on
request, but we will not be actively promoting it. We have also been able to
improve the performance and shelf life of Slide A+ as a result of what we
learned during the development of Slide AStar.
MS: Did you have any surprises during the development of the new
product?
RD: We first evaluated samples of all the commercially available
NH2
H2N
O aminosilanes. These are available with varying linker chain lengths and
numbers and positions of amino groups. We also put prototype coated slides
NH
O
through full DNA hybridization experiments to find out the best performing
surface under varying conditions. The way the aminosilane coating works is
that the negatively DNA is attached to the surface by ionic interaction with
positively charged amine groups. We had always thought that longer
aminosilane molecules with multiple amino-groups produce higher signal-to-
noise ratios, as their higher net positive charge will bind more DNA to the slide
surface. However, we found that the situation is actually more complicated,
and that while surfaces with a higher charge do bind more DNA, they are also
much more difficult to block effectively, resulting in significantly higher non-
specific binding. The higher levels of non-specific binding have a negative
effect leading to poorer signal-to-noise ratios. For this reason the aminosilane
used for Slide AStar is a very short-chained molecule.
MS: When will the new Nexterion® Slide AStar be available?
RD: We have already started sampling large customers, but the official
product launch will be at the Discovery-2-Diagnostics conference in San
Diego on October 20 2008, so watch this space!
© SCHOTT

4. The Nexterion® Newsletter #4 September 2008 page 4
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SCHOTT Guide to Selecting the Optimal Slide
Surface for your Protein Microarray
In January, Dr. Dietmar Knoll gave a presentation at the PepTalk 2008
conference in San Diego, CA, outlining some of the factors researchers
should consider when selecting suitable surfaces for functional protein
microarrays. The talk was well received, and was subsequently referenced in
an article in Genetic Engineering News (15th March 2008: “Protein Microarray
Uses Abound”). In the following article, Dr. Knoll discusses some of the key
points from the talk with “Microarray Solutions”.
MS: Why has SCHOTT dedicated so many resources to developing a
range of products for what is still a relatively small target market, when
compared to DNA microarrays?
Dr. Dietmar Knoll DK: Proteins are a very important class of bio-molecules to study as they
participate in every process within the living cell ,for example, as enzymes,
Senior R&D Scientist receptors, structural proteins, carrier proteins and so on. As a result, functional
SCHOTT Microarray Solutions protein microarrays have become the fastest growing part of the microarray
Jena, Germany. slide market, and are suited to a wide range of applications, such as
biomarker discovery, antibody and protein substrate profiling, and protein
Prior to this, Dietmar worked for
quantification in diagnostic assays. Microarrays provide a way of doing this in
Quantifoil Micro Tools, a small
a rapid, highly parallel, and cost effective way. However, when compared to
biotech company acquired by
DNA microarrays, there are still many technical challenges to overcome.
SCHOTT in 2003. He received his
Ph.D. in Organic Chemistry from
Leipzig University and has MS: What are some of the technical obstacles to creating function
extensive expertise in organic protein microarrays?
surface coatings. DK: One of the major challenges is the generation of the content itself. To
ensure accurate results, a stable protein is necessary, and finding or purifying
suitable high quality proteins can be costly in both time and money. Proteins
are much more complex than DNA, starting with the higher number of building
blocks to form polypeptides, continuing with a secondary structure, and finally
a more or less susceptible 3-D structure, which is essential for their function.
Because of the complexity of a protein, providing a stable environment to
maintain the structure is important for any kind of biological assay.
Consequently, slide surfaces play a vital role providing a support structure to
keep the protein molecules intact and functioning properly, and at a fixed
“Because proteins have location for interaction with another biological molecule.
slightly different requirements
to maintain their 3-D MS: What are the most important slide surface characteristics?
structure, for example
membrane compared to DK: Many of the slide surface characteristics important for DNA microarrays
cytosolic proteins, and not all also hold true for protein microarrays. These include planar surface, high
requirements can be optimally binding capacity, low non-specific binding, high sensitivity, low auto-
reflected by one “universal” fluorescence of the glass and compatibility with the process protocols.
slide surface, so the user has However, the stabilizing environment of the slide surface is of much greater
to choose the most suitable importance for protein microarrays, along with the need for high binding
slide surface solution for their capacity, tolerance to a wide range of print buffers, and the opportunity to
specific application.” analyze the arrays using label free detection systems.
Dr. Ruediger Dietrich, MS: What types of slide surface are currently available from SCHOTT for
Director of Research & protein microarrays?
Development at SCHOTT
Microarray Solutions. DK: The SCHOTT coated glass substrates can be categorized into either two-
dimensional (2-D) or three-dimensional (3-D) surfaces.
2-D Substrates provide a planar surface consisting of a chemical monolayer,
which actively immobilize protein molecules via epoxy (Nexterion® Slide E), or
aldehyde groups (Nexterion® Slide AL). These surfaces are normally very
robust and reliable, however 2-D substrates provide very little structural
support for the tertiary or quaternary structures of proteins. Consequently, this
© SCHOTT

5. The Nexterion® Newsletter #4 September 2008 page 5
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type of surface is usually most suitable for arraying more “robust” proteins like
antibodies, or in assays that do not require the protein probes to be
functionality active. Another point to consider is the high steric hindrance with
2-D substrates. This disadvantage can be circumvented by addition of
appropriate linkers to keep the probe away from the surface. The binding
capacity of 2-D substrates is generally significantly less than with 3-D.
P ro b e ty p e
Using 3-D Substrates overcomes both limitations mentioned above as their
multi-dimensional structure help to retain protein functionality and offer a high
binding capacity. Another advantage of these substrates is that the open 3-D
structure can provide the target with better accessibility to the printed probes.
S u rfa c e ty p e
3-D slide surfaces can be further divided into thin film and thick film coatings,
C o a tin g
thick films are typically tens of microns thick, whereas thin film typically have a
p ro p e r tie s
thickness of less than a few hundred nanometres. Thin film coatings such as
hydrogel slides (Nexterion® Slide H), Streptavidin-hydrogel (Nexterion® Slide
H-S) and polymer slides (Nexterion® Slide P), have higher binding capacity
than 2-D slides, and provide a exceptionally low non-specific binding after
R ecom m ended
N e x te r io n ®
blocking. Therefore, high signal-to-noise ratios, and sensitivity can be
p ro d u c t
achieved with these substrates. Examples of thick 3-D coatings are
nitrocellulose coated slides (Nexterion® Slide NC).
MS: During your talk you mentioned reverse phase assays, do these
require specific substrates?
DK: Yes, for reverse phase using cell lysates, the thin film hydrogel and
polymer surfaces are not really suitable. These probe types require high
concentrations of detergent to avoid precipitation, conditions that would result
in very large spot sizes and poor spot morphology on hydrogel and polymer
surfaces. Therefore the thick 3-D substrates like nitrocellulose coated slides
(Nexterion® Slide NC) are the substrates of choice for this application.
Generally, nitrocellulose slides are a good starting point for most protein array
applications as they produce a linear correlation between probe and target
over a wide concentration range. Another advantage is that for many
applications printed nitrocellulose slides exhibit a very long shelf life at
ambient temperatures without significant loss of activity. The disadvantages
discovered when evaluating nitrocellulose surfaces can include high
background, and no possibility of having additional layers such as, optically
active layers under the opaque nitrocellulose coating for enhancing signal or
use in label free detection.
MS: Do you have any final recommendations?
DK: The range of possible assays, technologies and studies involving analysis
of proteins is very diverse, and there is no one “universal” surface that will
work for all. Indeed the vast number of variables that can impact the quality of
data a user can generate from a protein microarray dictates that even the
above guidelines may not always be totally reliable. SCHOTT typically
recommending that users try a variety of different slide surfaces rather than
focus their efforts entirely on one slide surface. For additional advice on
selecting the most appropriate slide surface for your protein application, or to
receive a copy of the PepTalk 2008 presentation given by Dr. Dietmar Knoll,
please send an e-mail message.
© SCHOTT

6. The Nexterion® Newsletter #4 September 2008 page 6
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Epitome Biosystems Antibody Arrays
Epitome Biosystems, Waltham, MA: Ti-Tyr™ Profiling Chips for
Detection and Quantification of Site-Specific Phosphorylation via
Sandwich Immunoassays
Epitome Biosystems is pioneering innovative protein measurement products
to enable drug discovery, drug development and the practice of clinical
Company: Epitome Biosystems
Location: Waltham, MA medicine. The company's highly quantitative and specific protein
Web: www.epitomebiosystems.com measurement products provide critical information on biological mechanisms
Substrate Used: Nexterion® Slide H and reveal important biomarkers or readouts of cell function. Epitome’s initial
focus is on novel phosphorylation measurement products, including mass
spectrometry (MS)-based biomarker discovery, as well as profiling chips and
multiplex assay kits that are based on Epitome’s proprietary EpiTag™
technology. The EpiTag™ technology platform enables quantitative,
multiplexed and highly specific measurements of protein abundance and
amounts of phosphorylation at specific sites using targeted antibody pairs in a
peptide-based sandwich immunoassay format. Epitome’s Ti-Tyr™ Chip
provides quantitative profiling of dozens of phosphorylation sites
simultaneously, on up to sixteen samples per chip, using a standard
microarray reader. These products enable:
 Quantitative assessment of phosphorylation at individual sites on
proteins
 Analysis of on- and off-target drug responses across signalling
networks
 Measurement of low copy number proteins and low abundance
phosphorylation events
Epitome’s innovative protein measurement products and services enable
Pharmaceutical, Biotech and Academic researchers to obtain highly specific,
quantitative information about the cell-signalling network, which is a key
interface for monitoring drug action and understanding disease. Key
application areas include biomarker discovery and development, target
validation and elucidation of mechanisms of drug action.
The Ti-Tyr™ Profiling Chip is a tyrosine phosphorylation focused product,
based on Epitome’s proprietary EpiTag™ technology. Tyrosine
phosphorylation is measured quantitatively at a site-specific level, after
proteolytic fragmentation of samples. The Ti-Tyr™ Chip allows for multiplexed
analysis across 74 phosphotyrosine sites on 60 different proteins using a
planar microarray. The Ti-Tyr™ Chip covers a wide range of content including
receptors (e.g. EGFR and HER2), adapter and scaffold proteins (e.g. IRS1
and Crk), intracellular mediators (e.g. Erk1 and Raf-1) and transcription
factors (e.g. c-Jun and STAT3). A single chip can be used to analyze 16
different samples, including reference standards and controls, or four chips
can be mounted in a carrier and treated similar to a microtiter plate.
A number of coated microarray slides from several manufacturers were
evaluated on their ability to meet the demands of the Epitome application.
“SCHOTT slides were the only slides that provided uniform, high signals and
very low backgrounds necessary for our highly multipexed antibody arrays,”
reported Tim Nadler, Director of Product Development, Epitome BioSystems
SCHOTT slide quality enabled Ti-Tyr™ Chip’s ability to consistently perform
quantitative, high content measurements.
EpiTag™ technology provides a unique, powerful platform for targeted,
quantitative and highly multiplexed protein measurements. The approach
provides a predictable, streamlined path for assay development and enables
rapid content generation. In addition to ongoing Ti-Tyr™ Chip content
expansion, similar profiling chips incorporating threonine and serine
phosphorylation measurements are in development.
© SCHOTT

7. The Nexterion® Newsletter #4 September 2008 page 7
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SCHOTT Microarray Solutions News
New SCHOTT Microarray FAQ Section Goes Online
Since entering the microarray substrate market several years ago, SCHOTT
has aimed to provide customers with the best possible technical support,
whether it be through direct contact with designated technical support
specialists, or via support materials such as protocols, scientific papers or
customer references. To further enhance this offering, SCHOTT has just
launched a new Frequently Asked Questions (FAQ) section to be found at the
Nexterion® web site.
New Nexterion® Microarray Substrates Catalogue
The new catalogue for the Nexterion® range of microarray products will be
available from 01 September 2008. The format of the new catalogue will be a
flexible ring binder system, allowing customers to keep all the details of the
Nexterion® products, such as product flyers, ordering details, protocols etc., in
one place. The catalogue can easily be kept up to date simply by adding new
information sheets as they become available. The layout of the individual
product flyers has been redesigned to improve readability and allow
customers to find the important information quickly.
Nitrocellulose Slide Application Note
SCIENION AG manufactures and markets non-contact dispensing systems for
printing microarrays. They have recently published an application note
favourably comparing the new SCHOTT Nexterion® nitrocellulose slides (Slide
NC-W and NC-D) to the market leading nitrocellulose slide. For further details
please download the “sciFLEXARRAYER Application Note No. 08001” from:
www.scienion.de/innolino/pdfdownload.php?id=80
Nexterion® MPX 16-well Slide Price Reduction
The Nexterion® MPX 16-well slides have always been a popular way to run
multiple arrays on one slide. SCHOTT has now made these slides even more
cost effective by reduced the list price of all the MPX slides. In order to do this
the slide package now contains five MPX slides rather than eight, and the
Nexterion® 16-well self-adhesive superstructure and sealing strip are now
supplied as a separate item.
For more details about the revised MPX slide range please visit the SCHOTT
Nexterion® web site.
© SCHOTT

8. The Nexterion® Newsletter #4 September 2008 page 8
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Conference and Exhibition Calendar 2008/09
Exhibition Location Date
Discovery2Diagnostics Manchester Grand Hyatt October 20-22
San Diego 2008
One Market Place
San Diego, CA 92101 USA
PEPTALK 2009 Hotel Del Coronado January 12-16
1500 Orange Ave 2009
Coronado, CA 92118 USA
LabAutomation2009 Palm Springs Convention January 25-27
Center, Palm Springs, CA 2009
USA
Statusseminar Chip DECHEMA-Haus March 05-06
Technologies Theodor-Heuss-Allee 25 2009
60486 Frankfurt am Main,
Germany
Advances in Microarray Stockholm International May 19-20
Technology Fairs 2009
S-125 80 STOCKHOLM
Mässvägen 1,
Stockholm/Älvsjö, Sweden
Did you know?
By entering our competition, you will have a chance to win one Apple iPod
classic (80 GB).Simply answer the three questions below, and send your entry
to arrive before 12 midnight (CET) on 28 February 2009.
By email: coatedsubstrate@us.schott.com
By fax: +1-502/966-4976
The winner will be the first correct entry drawn at random.
Name : _____________________________________________
Email : _____________________________________________
Institute/Company : _____________________________________________
1. What title was the city of Jena awarded in 2008?
□ City of Optics 2008 - "Stadt der Optik"
□ City of Science 2008 - "Stadt der Wissenschaft"
□ City of Sport 2008 - "Stadt des Sports"
2. Which Nexterion® slide does Epitome Biosystems use for their
profiling chips?
□ Nexterion® Slide E
□ Nexterion® Slide H
□ Nexterion® Glass B
Microarray Solutions
SCHOTT North America Inc. 3. What is the name of the new aminosilane slide from SCHOTT?
5530 Shepherdsville Road □ ASpar
Louisville, KY 40228 □ APlug
USA □ AStar
Phone: +1- 502-657-4417
Fax: +1- 502-966-4976 * Only one entry per person. The judges' decision is final. This competition is void where
E-Mail: coatedsubstrate@us.schott.com prohibited. This competition is run and staged in accordance with German legislation.
www.us.schott.com/nexterion
© SCHOTT