3. Tekes – your contact for Finnish technology
Tekes, the National Technology Agency, is the main funding organisation for
applied and industrial R&D in Finland. Funding is granted from the state bud-
get.
Tekes’ primary objective is to promote the competitiveness of Finnish indus-
try and the service sector by technological means. Activities aim to diversify
production structures, increase production and exports and create a foun-
dation for employment and social well-being. Tekes finances applied and in-
dustrial R&D in Finland to the extent of about 400 million euros annually. The
Tekes network in Finland and overseas offers excellent channels for cooper-
ation with Finnish companies, universities and research institutes.
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tion and networking for companies and the research sector for developing
innovative products and processes. Technology programmes promote de-
velopment in specific sectors of technology or industry, and the results of
the research work are passed on to business systematically. The pro-
grammes also serve as excellent frameworks for international R&D coopera-
tion. In 2004, 25 extensive technology programmes are under way.
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ISSN 1239-758X
ISBN 952-457-167-6
Cover: LM&CO
Cover pictures:
EGFR-stained tissue section from lung cancer by Olli Kallioniemi and Guido Sauter.
Mitosis – normal bipolar human cell at metaphase (left) and two abnormal
mono-polar human Plk1 knockdown cells at metaphase-like stage (right)
by Marko Kallio. DNA (green), microtubules (red).
Two dimensional polyacrylamide gel by Laura Salusjärvi.
Page layout: DTPage Oy
Printers: Paino-Center Oy, 2004
4. Foreword
With the rapid increase in the significance of proteomics for the bioindustry, proteomics now offers
a base for applications in areas such as diagnostics and drug research.
This proteomics survey evaluates the status of proteomics in Finland and the significance of
proteomics for Finnish industry and research. The survey also outlines future developments needed
in Finland.
The National Technology Agency wishes to thank not only the authors of this report but also the
other people in industry and academia who have contributed to the work in several ways and thus
made it possible.
It is hoped that the report will meet the expectations of professionals and decision-makers, helping
them to focus their future actions for the best possible results.
April 2004
Tekes, The National Technology Agency
5. Executive summary
The discipline of proteomics, i.e. simultaneous analysis of
all the proteins in a cell at a given point in time, is undergo-
ing strong development and growth. The market is esti-
mated to be worth USD 2.9 billion in 2005. A recent report
by the Cambridge Healthtech Institute estimated the ex-
penditure on proteomics to increase by 15% to 50% in
2003, compared with 2002. Major areas of increase were
sample preparation (increase in two- and multi-dimension-
al liquid chromatography systems) and mass spectrometric
analysis. Of the estimated USD 2.9 billion proteomics mar-
ket in 2005, two-dimensional sample separation is ex-
pected to account for approximately 30%. Regarding pro-
tein analysis, 300% more mass spectra were expected to be
generated in 2003, compared with 2002. Interestingly, the
biggest increase in market value was envisaged for protein
chips.
In proteomics, Finland is lagging behind countries such as
Sweden, Denmark and Netherlands. There has been no fo-
cused investment to form bigger core facilities, as done in
other countries. In Finland, proteome analysis is mainly
performed in university laboratories whose remit is to
serve the needs of academic research. The Finnish biotech-
nology industry has not used the capabilities of proteomics
technology to full potential. This appears to be partly due to
poor awareness of the services available.
To achieve high throughput, proteomic methods need to be
further automated and standardised. New technology is
needed to accomplish this. Microarrays (e.g. protein or an-
tibody arrays) present an interesting technology platform
for future exploitation. The first protein chip products are
already on the market, and the field is expected to continue
to develop rapidly. So far, there is not sufficient content
(i.e. characterised proteins, antibodies, etc.) to be spotted
onto the chips. Protein arrays evidently possess high poten-
tial to resolve many of today’s unresolved bottlenecks in
proteome analysis. Array technology may open new ave-
nues for functional proteomics and, later on, for clinical
proteomics. The development of clinically relevant content
for next-generation proteomics and the application of new
technologies such as microfluidistics present additional fu-
ture business opportunities in Finland.
During the past few years, proteomics has evolved as intel-
lectual property-intensive activity. The number of
proteomics-related patent applications has doubled every
year since the early days of proteomics. The great majority
of the applications (60%) have been filed in the USA, fol-
lowed by Japan and Germany. Interestingly, China is
among the top four countries, in front of the United King-
dom and France. Finland lags behind in proteome patent
applications, too. As the field is young and developing rap-
idly, the rate of seeking intellectual property rights protec-
tion will probably be maintained at least at the current level
for some time.
In Finland, like elsewhere in the world, proteomics offers a
new means to improve the competitiveness of the
bioindustry. Proteomics can help to enhance the efficiency
and control of the processes used in the biotechnology in-
dustry to produce bioactive compounds. New targets for
drug development can be identified and validated, diagnos-
tics can be improved by proteomic profiling, and novel
biomarkers can be found. Applicable to the theranostics
and personalised medicine of the future, the more precise
biomarkers will bring diagnostic and clinical research ca-
pabilities to new levels. In Finland, these potentials in com-
bination existing sample collections, capabilities to per-
form clinical studies and clinical expertise offer additional
competitive edge.
Many Finnish companies would already benefit from the
new data obtainable by proteomics methods. The existence
and range of the current services would need to be better
communicated to Finnish companies. It is therefore pro-
posed that an open planning meeting be arranged to touch
off the communication between service providers and us-
ers. Furthermore, the services in Finland would need to be
developed further in terms of quality, robustness, through-
put and pricing. For the future, a new technology develop-
ment programme should be drawn up to take advantage of
the current business window in proteomics. With its clini-
cal expertise, potential for technology development, re-
agent manufacturing skills and software development ca-
pabilities, Finland is well geared to deal with this chal-
lenge.
6. Abbreviations
ADME-TOX administration, metabolism and toxicology studies
2D GE two dimensional gel electrophoresis
CAGR common annual growth rate
CAD collision activated dissociation
CID collision induced dissociation
DE delayed extraction
ECD electron capture dissociation
ESI electrospray ionisation
FTICR fourier transform ion cyclotron resonance
FWHM full width of half maximum
HPLC high pressure liquid chomatography
ICAT isotopic-coded affinity tag
IEF isoelectric focusing
IT ion trap
LC liquid chromatography
MALDI matrix assisted laser desorption/ionisation
MS mass spectrometry
MS/MS tandem mass spectrometry
MudPIT Multi-dimensional protein identification technology
PIE pulsed ion extraction
PMF peptide mass fingerprinting
PTM post-translational modification
Q quadrupole
QA quality assurance
rp reverse phase
SDS-PAGE sodiumdodecyl sulphate polyacrylamide gel electrophoresis
SCX strong cation exchange
SELDI surface enhanced laser desorption/ionisation
SID surface-induced dissociation
SILAC stable isotope labelling by amino acids in cell culture
TOF time-of-flight
7. Purpose of the report
This report provides an overview of proteomics today, discusses current trends and makes recom-
mendations on the focus of Tekes’ future contributions to the field. The report also summarises the
current proteomics capabilities in Finland and the needs of the Finnish biotechnology industry and
makes recommendations for addressing any unmet needs identified.
Data collection
This report is based on the results of fact-finding during the autumn of 2003. The authors visited the
proteomics core units of Finnish universities, interviewing staff. The authors also interviewed rep-
resentatives of many Finnish companies with an interest (but not necessarily activity) in proteomic
analysis. A web-based questionnaire survey was conducted among 75 Finnish and a few interna-
tional companies. In addition, the authors attended several key proteomics conferences and moni-
tored the scientific literature, relevant websites, commercial market reports and news items.
10. Proteomics
Proteomics is one of the new trends in biological science
that have emerged since the completion of the sequencing
of the human genome and the genomes of some other im-
portant organisms. Proteomics is defined as simultaneous
analysis of all the proteins in a given cell at a given point in
time.
Proteome: the complete protein complement ex-
pressed by a genome or by a cell or a tissue type
(Wilkins M. et al. Biotechnology 14: 61-5, 1996)
Genome sequencing and the introduction of deoxyribonu-
cleic acid (DNA) microarray technologies during the
1990s marked the start of the –omics era of research [1]. In
principle, -omics technologies are aimed at profiling the
entire pattern of information in a single experiment.
Proteomics is a logical continuation of the widely used
methodology of transcriptional profiling. The ultimate goal
of proteomics — to analyse all the proteins, including
splice variants and modifications, that participate in vari-
ous cellular processes — is still a dream and not possible
today. Nevertheless, the discipline of proteomics has de-
veloped significantly since its early days, and is showing
exponential growth in terms of numbers of publications
(Figure 1), patent applications (see Patenting) and market
size.
Compared with genomics, proteomics develops with a lag
of 10 to 20 years. Genomics is now reaching a plateau as far
as the number of publications per year is concerned and
still outnumbers proteomics by a factor of 10. Proteomics
publications have just increasing exponentially and could
well overtake genomics publications in coming years.
A global initiative to conquer the complexity of proteomic
analysis was launched in 2002. The proteome project of the
Human Proteome Organization (HUPO) is divided into
specific sections, such as the human plasma, liver and brain
proteome projects and the Proteomics Standards Initiative.
Genomics efforts led to complete sequencing of the human
genome (and those of many important other species) earlier
than expected. It was commonly thought that once the ge-
nome was done and ready, the efforts could be focussed on
new challenges, such as proteomics. It has turned out, how-
ever, that research and commercial ventures related to
genomics continue at an increasing pace and will do so
over the years to come, for instance in the sphere of protein
annotation. It can be concluded, given the much more com-
plex nature of proteomics, that proteomics is likely to con-
tinue as a field of active technology developments and new
business openings for many years to come.
Analytical needs
During the last decade, proteomics has attracted a lot of at-
tention from both the research community and the biotech-
nology industry. The field is characterised by rapidly in-
1
Publications in proteomics
0
200
400
600
800
1 000
1 200
1 400
1 600
1995 1996 1997 1998 1999 2000 2001 2002 2003
Year
Noofpublications
Publications in genomics
0
2 000
4 000
6 000
8 000
10 000
12 000
1975 1980 1985 1990 1995 2000 2001 2002 2003
Year
Noofpublications
Figure 1. Numbers of publications in proteomics (left) and genomics (right) per year according to the
PubMed database. The search terms were the year and the words ‘proteomics’ or ‘proteome’ and
‘genomics’ or ‘genome’.
11. creasing biological knowledge, strong technology devel-
opment and still unmet needs. In spite of new technologies,
particularly in sample separation and mass spectrometry
(MS), a number of important analytical needs have not
been fulfilled:
• Analysis of complex biological mixtures
• Ability to quantify separated protein species
• Sufficient sensitivity for proteins of low abundance
• Quantification over a wide dynamic range
• Ability to analyse protein complexes
• High throughput
• Robust, routine applications.
So far, proteomics has been mainly applied in basic re-
search but its use is increasing in the pharmaceutical, diag-
nostics and other biotechnology industries. In drug devel-
opment, the main applications are in target identification,
validation and the search of predictive administration, me-
tabolism and toxicology (ADME-TOX) profiles for drugs.
The methods used need to produce results that are reliable
and reproducible from experiment to experiment.
In diagnostics, proteomics methods provide means for de-
termining the proteome profiles of various types sample,
such as blood, serum, urine, tissue extracts and tissues. Pro-
tein profiles can offer improved diagnostic efficacy over
the protein markers used today. The same applies to identi-
fication of novel biomarkers for more specific and predic-
tive diagnostics and markers for personalised medicine. In
addition to the requirement of robustness, the commonly
used sample materials place additional demands on the
sample preparation phase.
In the biotechnology industry, e.g. research reagent pro-
duction, protein engineering and plant biotechnology,
proteomics can be applied to sectors such as process devel-
opment and control and metabolic engineering. Most valu-
able information is gained by a systems biology approach,
in which the various steps in the relevant cellular pathways
can be identified and optimised for particular purposes. An
additional requirement in this context is capacity for effi-
cient utilisation of bioinformatics.
With regard to conventional protein identification, the gap
between requirements and current capabilities is small. Of-
ten the issue is the quality of sample processing. In most
cases where there is enough material in the sample and the
proteins can be enzymatically digested, the analysis will
provide the answers required.
Analytical needs are harder to meet if more precise infor-
mation is desired about the functions and interactions of
proteins. Significant unmet needs exist in the bioinforma-
tics analysis of proteomic data, as well as in the integration
of the data with cellular pathways and cellular localisation.
Technology leverage should be improved to fulfil the re-
quirements in the various applications.
Proteome analysis scene
Traditionally, proteome analysis is often considered as a
separate entity. The research is focused on ascertaining the
role of each protein separately, case by case. Research
problems come in two categories:
1. What are the protein species in the sample, and what are
their amounts?
2. Is a particular protein present in the sample, and how is
it modified?
Typically, the purpose of a proteome analysis is to detect
all the proteins present in a sample. The current methods of
sample separation and analysis, two-dimensional gel elec-
trophoresis (2D GE) and liquid chromatography (LC) with
MS analysis, are geared towards achieving this goal. The
methods used, however, are still far from optimal. Identifi-
cation of the separated proteins and their subsequent modi-
fications is the main goal in conventional proteomics anal-
ysis.
In the second type of research, data about a specific protein
(or a set of proteins) is collected. The protein content of the
sample is correlated with a certain physiological state of
the organism, responses to various stimuli or other pertur-
bations. Specific functions are usually mediated through
post-translational modifications (PTMs), such as phos-
phorylations, acetylations or glycosylations, which places
additional demands on the sensitivity and precision of the
method. high throughput analysis of PTMs is extremely
demanding and not routinely available today.
Systems biology scene
Proteomics cannot be perceived as an isolated entity with
its own specific needs and technologies. As in all biologi-
cal processes, different levels of information are needed
about cells to detect the right responses to particular sig-
nals. In cells, genetic information is needed to translate the
appropriate responses to the protein level. Proteins (e.g. re-
ceptors, enzymes, structural proteins or signalling pep-
tides) are the main players in all cellular pathways. In the
various phases involved in cellular responses, proteins can
be cut, modified in a number of ways and excreted into par-
ticular compartments or into the extracellular space, for in-
stance the blood stream.
There is a great difference in complexity between pro-
teome analysis and genome analysis. The 35 000 human
genes, each of which encodes not only one protein but a
large number of various splice variants (having in part the
same basic amino acid sequence), with varying numbers of
other post-translational modifications, may give rise to a
100- to 300-fold number protein variants. Furthermore, as
the dynamic range of proteins is in the order of 108
to 10
9
,
2
12. the analytical methods used should be highly sensitive as
well as highly quantitative.
In short, cellular processes at the proteome level are highly
dynamic, with many interactions between appropriate pro-
tein species taking place at any given moment. Cell metab-
olism comprises, for instance signalling pathways, cell
proliferation, apoptosis (Figure 2) and the production of
metabolites for these cellular processes. Moreover, meta-
bolic processes are subject to feedback control, which adds
to the complexity facing the analytical effort.
Proteomics should not, therefore, be regarded separately,
but rather as an important element of the entire systems bi-
ology (Figure 3). The information gained from proteomic
analysis is most valuable when seen in the context of the
whole of systems biology. Such integration is mainly pur-
sued at academic research units.
As more proteome-level information is collected, includ-
ing comparisons between samples collected in disease and
health, novel biomarkers can be revealed. The information
is valuable not only for target validation but also for identi-
fication of new druggable targets. Proteomic profiling may
also yield ADME-TOX data earlier in the process of drug
development, allowing savings in time and money.
Proteomic profiling is also highly useful in identifying
better predictive and diagnostic markers, as shown for vari-
ous cancers [2, 18]. Proteomic profiles are increasingly ap-
plied to diagnostics. The sample matrices include, in addi-
tion to serum and blood, specimens such as urine, cells and
tissues. Although potentially containing large amounts of
relevant information, the proteins of interest are sometimes
present in very low concentration in the sample (for in-
stance in sera), requiring high-sensitivity detection. The
most abundant proteins in serum, such as albumin and
immunoglobulins, often have to be quantitatively removed
from the sample prior to assaying proteins of low abun-
dance.
In the future, when therapeutics and diagnostics are fully
exploited together for personalised medical applications,
proteomics will no doubt be one the key methods for devel-
oping appropriate markers.
3
Figure 2. The apoptosis pathway. [2]
13. For the conventional biotechnology industry, understand-
ing cellular processes is most important in sectors such as
production of metabolites in microorganisms. The indus-
trial processes can be further optimised and controlled uti-
lising knowledge of the key components in biochemical
pathways. Proteomics can help to develop healthier
nutraceuticals in food biotechnology and promote new ad-
vances in plant biotechnology.
Development of bioinformatics software tailored to spe-
cific needs is essential for realising the potential of pro-
teomics in various applications.
Finnish scene
With a few exceptions, proteome analysis in Finland take
place at research core facilities in universities. The services
of these facilities are mostly used by local research groups,
and their success is typically measured by the number and
quality of academic publications they help to produce. So far,
very few Finnish companies have utilised these services (for
details, see CURRENT CAPABILITIES IN FINLAND).
Finnish researchers have produced appreciably fewer pub-
lications referring to proteomics, than those in Denmark,
Sweden or Netherlands (Table 1).
In contrast to Denmark and Sweden, there has been no con-
certed programme or investment in proteomics in Finland.
A number of smaller investments have been made in pro-
jects dealing in part with proteomics. The infrastructure for
high throughput proteome analysis is poorly developed in
Finland, and thus such analyses are not performed. Never-
theless, a demand for high throughput proteomics also ex-
ists in Finland.
4
Genomics and
transcriptomics
Proteomics Interactomics Phenomics
Systems biology
Proteomic analysis
Figure 3. Proteomics in systems biology.
Country Number of publications
Denmark 100
Finland 12
France 178
Germany 364
Iceland 1
Italy 93
Netherlands 57
Norway 6
Russia 8
Sweden 107
Switzerland 142
UK 350
USA 1565
The search terms were ‘proteome’ OR ‘proteomics’ combined
with country name based on author affiliation.
Table 1. Numbers of publications in proteomics
in selected countries according to the PubMed
database on 8 January 2004.
14. Summary of the world market
Several market surveys have been published on proteomics
in recent years. All of them report a substantial increase in
the proteomics market. The Proteomics Survey Report
2003 by the Cambridge Healthtech Institute estimated the
expenditure on proteomics to increase by 15% to 50% in
2003, compared with 2002. Major areas of increase were
sample preparation (increase in two- and multi-dimen-
sional LC systems) and MS analysis. The respondents of
the survey expected to be generating 300% more mass
spectra in 2003, compared with 2002.
Two-dimensional (2D) sample separation accounted for
about 30% of the estimated USD 500 million proteomics
market in 1999. According to a Frost and Sullivan market
survey, this share of 2D is estimated to be maintained in
2005. Interestingly, the biggest increase in market value
was envisaged for protein chips (Table 2).
The recent Protein Biochips report by Select Biosciences
(2003) concluded that in 2002, Biacore dominated the
USD 100 million market in protein chips, with Ciphergen
in second place. At an annual growth of 36%, the total mar-
ket in 2007 was estimated at USD 430 million, with some
new companies entering the field.
It can be concluded that due to the unmet customer needs,
proteomics will experience significant growth over the
coming years. Some of the technological factors contribut-
ing to this are:
• Developments in one- and two-dimensional gel electro-
phoresis
• Rapid increase in multi-dimensional LC technologies
• Developments in matrix-assisted laser desorption/ionis-
ation (MALDI) time-of-flight (TOF) and electrospray
ionisation (ESI) quadrupole (Q) TOF instrumentations
• Increased interest in protein chips as a future technol-
ogy.
In addition, the market is driven by pharmaceutical compa-
nies’ investments in research and development (target dis-
covery, validation and biomarker identification schemes).
During the past two years, numerous successful studies on
the identification of new, better biomarkers have been pub-
lished. These advances, together with the effects of the in-
tegration of diagnostics and therapeutics (theranostics),
will significantly increase the demand for proteomics in the
future.
5
Domain 1999 (millions of USD) 2005 (millions of USD) CAGR¹ (%)
Total proteomics 136 880 37
2D electrophoresis 21 444 66
Protein arrays 458 2 884 36
World Proteomics Market, Frost and Sullivan, 2000. ¹Common annual growth rate
Table 2. Proteomics market by application.
15. Technologies
The sample separation step is undergoing active technolog-
ical development. 2D GE is still the most widely used
method, efficiently separating proteins, their variants and
modifications (up to 15 000 proteins in one run). However,
in addition to certain limitations (with regard to membrane
proteins, for instance), the method is relatively complex
and lacking in robustness and standardisation. Recently,
multi-dimensional LC methods have been developed to
fulfil some of the unmet needs. Coupled with mass spec-
trometry, these methods allow efficient separation and iden-
tification of proteins, even membrane proteins can be more
readily analysed than using 2D GE. Multi-dimensional LC
methods typically allow approximately 1 500 proteins to be
detected in a single sample. These methodologies still re-
quire development in features such as robustness, repro-
ducibility, separation efficiency and throughput. For opti-
mal result, 2D GE and multi-dimensional LC are today
used in parallel.
In addition to sample preparation issues, major technologi-
cal bottlenecks exist in the analysis phase. The current soft-
ware does not fully meet requirements. Especially in runs
involving several complex biological samples, as is often
the case in studies of cellular pathways or novel bio-
markers, data validation and dataset linking steps presents
limitation in the efficiency.
MS is the key to protein identification in proteome analy-
sis. Because a proteome is a very complex mixture contain-
ing all the proteins expressed in a cell, rigorous separation
prior to MS is crucial. These two steps — separation and
MS — determine the quality of the outcome.
Separation
There are two approaches to separation, the traditional and
the modern. The traditional way is to carry out the separa-
tion ‘offline’ with regard to MS, whereas the modern way
is to separate the sample ‘online’ with MS [3]. In the for-
mer approach, the extracted proteins (intact or denatured)
are separated (Figure 4), but in the latter, the extracted pro-
tein mixture is first digested with enzyme and the resultant
peptides are then separated (Figure 5). The final situation is
the same in both cases: peptides from proteins are analysed
with MS and the proteins are then identified with
bioinformatics tools, provided that the data acquired are
adequate and the proteins (or their homologues) exist in the
database.
Traditional separation uses 2D sodium dodecyl sulphate
polyacrylamide gel electrophoresis (SDS-PAGE). Until
MS methods became available, proteins were identified us-
ing isotopic labelling, Edman degradation and immuno-
blotting. 2D GE can separate routinely over 1 000 proteins
(Figure 4). The two dimensions of the gel are isoelectric fo-
cusing (IEF) and polyacrylamide gel electrophoresis. In
7
Figure 4. Workflow of 2D GE-based proteomics.
16. IEF, proteins are separated according to their isoelectric
point. The result is a protein map in which ideally each pro-
tein has unique coordinates. In practice, there are usually
many proteins in one spot. Sample preparation is decisive
in 2D SDS-PAGE. Salts and detergents can affect IEF sep-
aration, slight changes in sample preparation can impair
reproducibility. Because use of detergents is limited, hy-
drophobic membrane proteins are difficult to examine.
Today 2D is the most powerful separation technique for
proteomics. A great deal of effort has been devoted to im-
proving quantification, reproducibility, acidic and basic
side IEF, yield of membrane proteins and separation. Ac-
cording to recent proteomics conferences, 2D gels can pro-
vide the researcher with a very good view of the cell
proteome. The pH range is nowadays 2.5—12, which cov-
ers all predicted Escherichia coli proteins, and the IEF
strips can be down to one pH unit in width. 2D gel electro-
phoresis is now a routine method, but there is still room for
optimisation and improvement. A good example of a re-
cent innovation is liquid-phase IEF as a prefractionation
tool before the first dimension of 2D gel electrophoresis
[4]. This allows at least 10 000 to 15 000 separate proteins
to be analysed, including proteins of very low abundance
(sensitivity =1 000 copies of protein/cell).
Despite the very good separation power and sensitivity of
2D GE, the technique is overall cumbersome, difficult to
fully automate, inefficient in case of membrane proteins,
and labile in terms of reproducibility. Every single sample
needs to be optimised, which can be very time consuming.
There is a demand for gel-less separation systems. Various
LC-based applications have been developed but almost in-
variably the protein mixture must first be digested to pep-
tides. Peptides, also the ones which originate form mem-
brane proteins, behave more uniformly than proteins dur-
ing separation. This is why membrane proteins can be ana-
lysed more efficiently as peptides.
Another approach to analysing proteomes without gels is
‘shot gun’ analysis using multi-dimensional protein identi-
fication technology (MudPIT) [3]. The idea is to use two
different chromatographic separations, for example strong
cation exchange (SCX) chromatography as the first dimen-
sion and reverse-phase high-pressure liquid chromatogra-
phy (HPLC) as the second dimension, and find as many
peptides as possible. The HPLC is online with MS, and the
system functions as in normal LC-MS/MS- analysis.
Quantification is always an issue in MudPIT analysis. MS
is not a very quantitative method, quality and quantity of
the spectrum depending heavily on running conditions and
8
Figure 5. ICAT protocol (left) and a pair of isotope peaks in an MS spectrum
(right). Printed by permission of David Goodlett.
17. the nature of the sample. If the soluble, peripheral and inte-
gral membrane protein fractions of a cell lysate are ana-
lysed separately, this technology can detect approximately
1 500 proteins. Preliminary quantification can be achieved
using special algorithms. Such experiments require special
computer programs which are usually individually written
in each laboratory. The data handling and processing is de-
manding. There has to be a computer cluster for analysis
and a laboratory information management system (LIMS)
for handling everything — and finally disc space to store
all the acquired data.
Labelling methods have been developed to improve quan-
tification. Isotope-coded affinity tagging (ICAT) [5] (Fig-
ure 5) is commercially available and may be one of the
most widely used technologies. ICAT uses a light and a
heavy form of the isotopic reagent to label reference and test
samples, respectively. The analytes are quantified by MS on
the basis of the intensity difference between the pair of peaks
obtained (Figure 5) and identified on the basis of a sequence
tag produced from one of the peaks. The Labelling reagent
also contains an affinity tag (biotin), which allows pre-puri-
fication of the biotin-labelled peptides prior LC-MS/MS
analysis. The reagent has the disadvantage of only labelling
cysteines. In yeast, about 90% of proteins are cysteine-con-
taining, leaving about 10% of proteins outside analysis.
ICAT is not alone sufficient for proteome analysis.
In response to the significant loss of material during ICAT
analysis, several other isotopic and non-isotopic label sys-
tems have been developed. One of the protocols is based on
14
N vs.
15
N metabolic labelling [6]. Automatic spectra pro-
cessing can present problems in this system, since peptides
contain different amounts of nitrogen, leading to a variable
mass difference between peak pairs. Metabolic labelling
can also be accomplished using stable isotope labelling by
amino acids in cell culture (SILAC) [7]. In this method,
there are two types of growth medium: one is normal and
the other contains an amino acid (e.g. Leu, Arg) labelled
with a stable isotope (1
H,
13
C or
15
N). The ‘control’ and
‘test’ cells are grown in these two media, proteins are
pooled after lysis, digested, separated and then quantified
and identified by MS as in ICAT. A single peptide may
contain more than one isotopically labelled amino acid,
and the mass difference between peak pair is therefore vari-
able, but the situation is in any case simpler than that with
15
N label. Metabolic labelling is not applicable for clinical
studies but for example in University of Colorado Health
Science Centre they had produced a metabolically labelled
mouse.
A recently invented method uses ‘mass defect’ tags to help
distinguish labelled peptides from background noise [8].
The mass defect originates from differences in nuclear
binding energies between the tags and biomolecules. The
biggest energy difference compared with biomolecules oc-
curs in elements with atomic numbers between 17 (Cl) and
77 (Ir). Mass defect labels can be detected in very complex
biomolecular backgrounds by MS, actually eliminating all
noise in spectra. Using stable isotopes of the above ele-
ments, same kinds of peak pairs can be obtained as with
any isotopic labelling protocol. Although not yet well es-
tablished, the technique may present a useful option for
multi-dimensional LC-based proteome separation.
Mass spectrometry
A mass spectrometer consists of two parts: the ion source
and the analyser. Both of these components set limits on
the analytical procedure and the accuracy of the result.
Two main ionisation techniques are used in proteome anal-
ysis, but there is greater variety in analysers.
Ionisation
The two widely used ionisation techniques are MALDI and
ESI. The starting phase is solid in MALDI and liquid in
ESI. Both techniques use soft ionisation, meaning that
protonation without fragmentation is the main ionisation
mechanism but adduct formation is also common. Frag-
mentation can be seen when molecules’ internal energy is
increased during ionisation by adjusting certain parame-
ters. While both are suitable for proteins and peptides, the
actual application depends on the analyser.
The basic principle of MALDI is described in Figure 6. The
most important factor in MALDI is the matrix. The matrix
is an organic molecule, usually a conjugated system, that
absorbs energy at the laser wavelength (normally 337 nm).
Sample and matrix are mixed together and the mixture
dried on a MALDI plate. When the laser hits the sample,
the matrix absorbs energy, ionises and evaporates carrying
the sample molecule to the gas phase.
Surface-enhanced laser desorption/ionisation (SELDI) is
based on the same general principle as MALDI. The only
difference is that the plate in SELDI is coated with ion
exchanger, hydrophilic or hydrophobic material or immo-
bilised antibody. SELDI’s main asset is that there is no
need for actual separation prior to MS, intact proteins in the
sample being profiled according to differences in their
physical or immunological interactions. Today, SELDI is
used mainly in biomarker research.
ESI is based on ions in (aqueous) solutions, only the sur-
rounding liquid is evaporated. In ESI, the solution contain-
ing charged ions flows through a capillary or needle held at
high voltage (Figure 7). From the tip of the needle, the so-
lution enters the ESI chamber as a fine aerosol of highly
charged droplets. These droplets are desolvated using
heated drying gas, and when the electrostatic repulsion
overcomes the surface tension, individual multiply-
charged molecule ions begin to form. These ions then enter
the mass spectrometer through a lens.
9
18. Sample purity is crucial in both ionisation methods. Deter-
gents, salts, etc. suppress ionisation at very low concentra-
tions, MALDI being somewhat less sensitive to salts and
some detergents. The dissimilarities in the techniques are
reflected in sample preparation before MS. ESI is mostly
used in combination with a nanoHPLC interface, whereas
MALDI is used without further separation. Recently the
full power of MALDI has become evident. In HPLC ESI,
there is a lot of material coming out, and there is concern
that something may be missed during the MS run, as pre-
sented recently for MALDI-TOF/TOF vs. ESI-Q/TOF [9].
When nanoHPLC is applied to complex peptide mixtures
(e.g. in ICAT or other labelling systems), large amounts of
material are lost if online ESI-MS/MS is used. When the
fractions are collected from LC directly onto the MALDI
plate, more peptides and proteins can be identified because
the analysis is not time-dependent — the sample is on the
target plate, and one sample may be analysed as long as de-
sired without fear of losing something. MALDI tandem
mass spectrometry (MS/MS) instruments can improve the
identification yields of proteomics samples.
Analysers
High mass accuracy and resolution are essential in
proteome analysis. The most widely used analyser types
are TOF, Q, ion trap (IT) and Fourier transform ion cyclo-
tron resonance (FTICR) and their combinations (Q/TOF,
TOF/TOF, QqQ and QIT). Ion mobility techniques have
also been introduced to proteomics for pre-separation be-
fore further analysis. Traditionally TOF (and TOF/TOF) is
used with MALDI and the others with ESI; FTICR can be
integrated with practically any ion source. Nowadays the
10
Figure 6. The principle of MALDI. Printed by permission.
Figure 7. A schematic example of ESI. Entrances to MS differ according to instrument.
19. situation has changed, with MALDI-Q/TOF being commer-
cially available and IT or TOF being possible to integrate at-
mospheric-pressure MALDI (AP-MALDI). ESI-TOF- in-
struments have also been on the market for some time.
In recent years there have been major improvements, like re-
flector and delayed extraction (DE), which have improved
TOF detector sensitivity and accuracy. As a result, TOF is
now commonly used in MS and MS/MS equipment such as
MALDI-TOF (commonest), Q/TOF and TOF/TOF. In TOF,
ions are separated according their flight time in a flight
tube (Figure 8). Because acceleration energy is the same
for all ions, bigger ions acquire lower and smaller ions
higher kinetic energies. The smallest ions therefore reach
the detector first and the largest ones last. Sometimes TOF
is called oTOF to indicate the orthogonal configuration of
the flight tube.
Analysers can be either MS setups like MALDI-TOF or
MS/MS setups like Q/TOF. With MS only total ion content
of sample can be measured, but with MS/MS one of the
ions of the sample can be isolated and fragmented and the
fragments (daughter ions) detected. MS/MS allows peptide
sequences, or at least parts (sequence tag) of them, to be de-
termined. Figure 9 presents a schematic illustration of a
Q/TOF instrument, showing the principle of MS/MS. The
11
Figure 8. MALDI-TOF instrument.
Figure 9. Q/TOF.
20. ion of interest is first isolated in Q and then transferred into
a collision cell. In collisions with inert gas molecules (Ar or
He), the parent ion fragments and forms daughter ions which
are further analysed in the TOF section. This is called colli-
sion-induced/activated dissociation (CID/CAD). The frag-
ments yield structural information about the molecule stud-
ied, for instance the amino acid sequence of a peptide (Fig-
ure 10).
Another tandem instrument in widespread use is IT. In IT,
ions are trapped in the centre of the electrodes of the trap
where ions, which are detected, can be stored for a long
time. IT can be used as an MS/MS instrument because the
selected ion can be isolated after detection. IT and FTICR
are exceptional in that the analysis is not limited to MS/MS
experiments but can be continued with MSn
systems
(MS/MS = MS2
). In this way, for example the complete
peptide sequence may be determined even if the MS/MS
outcome has been inadequate. The drawbacks of the instru-
ment are its modest resolution and mass accuracy.
FTICR deserves special mention. It is the most compli-
cated MS analyser — and the best. The physical back-
ground of the analyser has been published elsewhere [10].
In short, the basic principle is that ions are trapped in a
chamber located in the centre of a high magnetic field (typ-
ically 4.7-9.4 T). What makes this equipment superior, is
that it can provide a resolution of over 1 000 000 FWHM
(full width of half maximum); a figure of 3 300 000 FWHM
has been reported [11]. Such high resolution enables exact
mass calculations of intact proteins and conformational
studies to be carried out. FTICR has been claimed [11] to
be able to separate peptides differing by as little as
0.45 mDa from each other. By way of comparison, the
mass of one electron is 0.55 mDa and that of one proton is
1 Da. Further details on FTICR, its resolution power and its
proteomics applications can be found in the literature [11,
12, 13, 14]. As a new feature to the traditional instrument,
electron capture dissociation (ECD) can be used to frag-
ment whole proteins with good sequence coverage and ac-
curate characterisation of post-translational modifications
[13]. Although FTICR is complex equipment, it has lately
become more user-friendly and is today recognised as a
very powerful tool in proteomics research [14]. Its attrac-
tion is slightly diminished by the relatively high price and
maintenance costs.
Ion mobility is a recent newcomer in proteomics research.
In ion mobility applications, ions are pulsed through an
electric field and separated according to their three-dimen-
sional structure. It has been applied to MALDI-TOF in the
form of MALDI-ion mobility-SID-oTOF in which ions are
pre-separated on the basis of mobility, fragmented by sur-
face-induced dissociation (SID) and the ion fragments ana-
lysed by TOF. According to McLean [14], the ion mobility
step enhances the signal in the case of impure samples and
is also able to separate post-translationally modified pro-
teins/peptides [15]. Instrumentation suitable for proteo-
mics is commercially available but the full applicability of
the method remains to be seen.
Protein identification, software and
automation
The key of identification is that the DNA sequence coding
for the protein is known and exists in a database. For an or-
ganism with an incompletely sequenced genome, proteins
may be identified according to homology. The process of
identification varies slightly according to the type of equip-
ment and whether homologous proteins are sought. There
are also dissimilarities between the traditional and the more
recent procedures in proteomics. A very detailed review oft
MS methods and bioinformatics has been described else-
where [16].
For protein identification, interesting spots on a gel are ex-
cised and processed further prior to MS. Samples from gels
can be analysed in two ways. The simplest, fastest and
most popular way is peptide mass fingerprinting (PMF) or
mass mapping analysis using MALDI/TOF. The second
method, sequence tag analysis with reverse-phase nanoLC-
MS/MS, is slower but often more effective (for instance
when studying unsequenced organisms).
PMF is based on enzymatic cleavage rules, which is why
highly specific enzymes, e.g. trypsin, are preferred. Tryp-
sin cleaves the protein backbone whereby almost every
protein, even very homologous ones, yields a unique pep-
tide pattern, akin to the fingerprint of a human being. Be-
cause of this uniqueness, PMF is not suitable for identifica-
tion of the protein product of unsequenced genomes. The
tryptic peptides are scanned by MALDI/TOF (see spec-
trum in Figure 4), and the peptide masses are entered into a
search engine. The search engine virtually digests all the
proteins in a database (SwissProt, NCBI, own) and com-
pares the measured masses with the virtual ones. If a theo-
retical peptide is close enough to a measured one, the pep-
tide is marked as ‘matched’ (Figure 4). Search engines cal-
culate probability scores on the basis of matched peptides.
If many peptides are found in the same protein, the engine
reports a high-score identification. The identifications are
never 100% certain, so it should always be evaluated
whether the match is real or not. The probability is related
to mass accuracy: the better the accuracy, the smaller the
errors in the searches and finally the more reliable the re-
sults.
Sequence tagging can be performed with MS/MS equip-
ment. The tryptic peptides are usually separated and con-
centrated by nanoLC and analysed online with automated
MS/MS. In the collision cell, peptides are usually cleaved
at the peptide bond, and the peptide sequence can be read
from the ion series of the spectrum — if the acquired data
are good enough (see Figure 10). Sequence tags can be sub-
12
21. mitted to the same kinds of search engine as the tryptic pep-
tides in PMF. Identification is based on enzyme specificity,
parent ion (tryptic peptide) mass, amino acid sequence and
fragment ion masses. The last item means that not only the
amino acid sequence is important but also the place of the tag
in a peptide. For example, the peptides IAGGTAMPTGR
and ITGGTAMPAGR have same mass but different ion
series, thus producing different identities. In this way, a
protein can be identified with high probability based on
only one good sequence tag. For unsequenced organisms,
searches can be done on the basis of plain sequence infor-
mation, trying to find homologous proteins. In these cases,
there must be more than one good sequence tag to get reli-
able results.
PMF is not applicable to modern shotgun proteomics, as
the peptides are not derived from a single protein. Peptides
from different proteins are completely mixed, and they en-
ter MS in a sequence determined by their behaviour in SCX
and reverse-phase LC. The fundamental idea of shotgun-
analysis is to sequence as many peptides as possible and
identify as many proteins as possible. Identifications are
done like in any other sequence tag analysis, but the pro-
cessing system has to be powerful and the search engines
local because there is substantially more data produced by
one run and one experiment consists many LC runs. If la-
belling technologies are included or relative quantities are
desired, extra processing in form of normalisation and peak
pair correlation is needed. This often requires contribution
from information technology specialists to render the soft-
ware more efficient and functional.
Nowadays higher throughput is pursued in every field, and
automation has also entered the proteomics scene. There
are many steps worth automating, such as spot picking and
digestion (Figure 4). If sample handling is automated, the
MS side has to follow suit. While the same requirements
apply to sample handling software as to any robotics sys-
tem, the situation is different with regard to MS. The tech-
nical issues in MS have been largely solved in recent years,
leaving just some optimisation to be done, but now the
problems are in data processing. Autovalidation of noise
reduction and peak selection can still be a problem because
of software limitations. Unsequenced proteins pose prob-
lems for automatic identification. One of the most severe
problems is the mismatch between customer needs and the
software supplied by the instrument manufacturer, and
skilled programmers are therefore often needed when set-
ting up protocols for automated spectra processing or shot-
gun proteomics. Despite the various problems on the MS
side, many foreign proteomics laboratories are now high
throughput facilities (Appendix 1).
13
Spot 1108
560 580 600 620 640 660 680 700 720 740 760 780 800 820 840 860
m/z0
100
%
00jul1001 223 (36.892) Cm (221:226) 2: TOF MSMS 731.88ES+
26771.542
658.445557.395
639.463
593.279
575.296
622.345
594.313
648.469
692.302659.444
732.039723.419
764.582
772.558
870.697
781.498
870.454
852.492805.310
Spot 1108
880 900 920 940 960 980 1000 1020 1040 1060 1080 1100
m/z0
100
%
00jul1001 223 (36.892) Cm (221:226) 2: TOF MSMS 731.88ES+
161042.706
1042.592
927.687
870.697
888.603
888.392
916.445
907.365
928.693
928.801
1024.736
1016.561
990.415
986.670
1113.709
1043.735
1044.725
1113.590
1085.6331078.031
Figure 10. Example of sequence tagging. The graph shows an ion series starting at 1113,709 Da and
ending at 557,395 Da, originating from the sequence [1113,709]T-I/L-V-G-D-A[557,395].
22. Trends
The trends presented in the following are based on infor-
mation gathered at conferences, by web survey, in inter-
views with representatives of Finnish universities and cho-
sen biotechnology companies (Appendices 2) and from
other public sources. A global view presented at the HUPO
Annual Meeting in October 2003 was that proteomics
needs better technology to see more than the tip of the ice-
berg. This could be achieved by improving current technol-
ogy, e.g. by miniaturisation, but there is also room for new
breakthroughs (Table 3).
Separation
The recent trend has been a shift from 2D GE to gel-less
chromatography systems, but at the same time there have
been major improvements in 2D gels. In analysis of
cytosolic proteins, 2D gels are more powerful than 2D
chromatography, as pointed out in the Technologies sec-
tion above. On the other hand, 2D chromatography can be
more effective when studying membrane proteins. Analy-
sis on the gel and chromatography front has moved towards
analysing sub-proteome elements, e.g. organelles. The aim
at present is to simplify sample mixtures by pre-fraction-
ation, so that the resolution power of separation technolo-
gies will not be a limiting factor.
As offline LC-MALDI-TOF/TOF has proved more effec-
tive than online LC-ESI-Q/TOF, chromatography-based
methods can become more powerful in the near future, par-
ticularly in combination with labelling systems. 2D chro-
matography systems may also increase in popularity be-
cause of the introduction of fully automatic ‘LC-LC’
equipment on the market. Analysis can be done online with
ESI, or fractions can be collected on a MALDI plate.
Mass spectrometry
MS issues are discussed in detail in the Technologies sec-
tion above. Big inventions were made in the early 1990s,
and after 1995 MS technology has been the main develop-
ment area in proteomics. Many high-quality instruments
were introduced during the past decade, and now the focus
15
Process phase Trends
Separation Pre-fractionation, to decrease the sample complexity
Organelle sub-proteomics
LC-MS/MS automation
MS Automation increases
Hybrid systems are developed further
MS imaging is evolving
Bioinformatics and automation Turn-key solutions still missing
Data handling and integration
Automation of present methods
PTMs and serum proteome New methods for high-throughput PTM analysis needed
Serum proteomics for new biomarkers is evolving
Biochip technologies Rapidly emerging field
A few established companies, but a number of
newcomers
Various platforms under development
Chip content still a problem
Table 3. Trends in proteomics.
23. is on software development. Improvements are naturally
being made all the time, and new hybrids are formed (cf.
ion mobility), but the main emphasis today is on automa-
tion. Various mass spectrometric systems are also now be-
ing applied to particular types of analysis, for example tri-
ple quadrupole (QqQ) is still found to be very good in
phosphorylation studies, IT is best when high scanning
speeds are needed, MALDI-TOF/TOF is ideal for high
throughput protein identification, and FTICR and Q/TOF
are methods of choice when accuracy is an issue.
Recently, MALDI has been used to image tissue specimens
directly. This gives the possibility of simultaneous ‘image’
and analysis of proteins in various locations [17].
Software and automation
high throughput systems will speed up the analysis of the
huge numbers of proteins in a cell. As discussed in the
Technologies section, sample handling in 2D gels and
chromatography systems can be quite easily automated but
the MS side can present problems. MS automation actually
boils down to software and programming. As people are
starting to realise how multiplexed and useful information
a mass spectrum can provide, the next task is to produce
spectrum interpretation and processing scripts to hasten
analysis. People in laboratories have previously produced
their own scripts but now manufacturers, too, have woken
up to reality. A couple of years ago, the main trend was im-
provements in instrument technology, now customers de-
mand more versatile software and more features to be re-
ally able to dig out the meaningful data.
It is potentially problematic that while the software pro-
vided by an equipment manufacturer may not match cus-
tomer needs and another manufacturer may have a better
solution for the customer’s application, the customer can-
not grasp the latter offer without being charged high
licence payments for a couple of extra software features. In
some cases, data cannot be converted to the required soft-
ware format, or there are other limitations. For example,
the powerful BioWorks software package from Thermo
Finnigan is designed for IT data, and use of the software
with systems such as Q/TOF will yield less than optimal re-
sults.
Recently Agilent Technologies released ‘new-generation
software’ called Spectrum Mill. With Spectrum Mill, raw
data from practically any manufacturer’s (not Bruker’s)
equipment can be converted, and instrument type can be
selected for optimising the results. The software can handle
MALDI data, normal MS/MS data, multi-dimensional
chromatography runs and ICAT experiments, and it fea-
tures a de novo sequencing tool and a basic modification
search mode. It is originally built on the ProteinProspector
search engine by Millennium Pharmaceuticals (Carl
Clauser), and Agilent has develop it further. Spectrum Mill
looks very promising (personal experience) but whether
the algorithms really work and give representative results
remains to be seen.
Post-translational modifications and
the serum proteome
It is well known that phosphorylations play a very impor-
tant role in cell signalling, and the emergence of phos-
phorylation analysis as part of proteomics research is
hardly surprising. Depending on the available MS instru-
mentation, there are many routine ways to study phos-
phorylations. Still, the results have proved to be rather
poorly reproducible. Other physiologically important mod-
ifications, such as glycosylation, are even more challeng-
ing, and there are several projects underway aimed at more
sophisticated PTM analyses.
Another problematic area is the study of proteomes of bio-
logical fluids, serum being a good example. In serum, the
dynamic range of proteins is huge, and the most interesting
proteins are present at very low abundances (originating
from tissue fluid leakage, for instance). These interesting
proteins make up only about 1% of all serum proteins. If
analysis of serum is attempted in the traditional way, a 2D
gel reveals only a fraction of all the different proteins be-
cause the most abundant proteins — albumin, transferrin
and immunoglobulin — mask the others. Today, depletion
kits are used to remove the abundant proteins but there is
also a need for more sophisticated methodology.
Biochip technology
DNA-chip technologies have attracted both the scientific
and financial community in recent years. Several new com-
panies have entered the protein array field (Appendix 3).
The common theme is miniaturisation and the potential to
perform a large number of tests in a small device. The main
application area has been expression profiling, where chips
have offered a means for simultaneous analysis of thou-
sands of hybridisation reactions. Nevertheless, proteins
and their interactions with other proteins, nucleic acids and
small molecules are based on much more complex reaction
principles, requiring further development efforts to obtain
the sensitivities and specificities needed.
Some companies have introduced protein arrays (Appen-
dix 3) aimed not only at proteomic analysis but also func-
tional analyses of proteins (e.g. Biacore AB, Ciphergen
16
24. Biosystems Inc., Phylos Inc.). Protein arrays will become
more important tools, once the content is more readily
available. Large projects, such as the Affinity Proteomics,
aim to produce antibodies to every protein expressed by the
human genome. These will be characterised against puri-
fied antigens and tested on tissue arrays to collect informa-
tion about their specificity for tissue antigens. Companies
are focused to produce various binding partners, e.g.
affibodies, monoclonal antibodies and their fragments. Pro-
tein arrays can also provide functional information about the
cell proteome, thus promoting knowledge at systems biol-
ogy level.
In addition to the common issues related to miniaturisation,
such as optimal surface chemistry, sample preparation,
sampling error and sensitivity, detection also warrants con-
sideration. Although fluorescence labelling is still the com-
monest detection method with protein arrays, MS-based
technologies, e.g. SELDI, have also been recently used to
analyse proteins in arrays. MS has one big advantage over
fluorescence: the bound agent can be identified straight
from the array. In antibody arrays, where unknown anti-
gens are fished from cell lysates, MS could be really pow-
erful.
17
25. Patenting
The number of proteomics-related patent applications has
doubled every year since 1995, and by 2002 approximately
one thousand patent families had been filed (Figure 11).
The great majority of the applications (60%) have been
filed in the USA, followed by Japan and Germany (Figure
12). Interestingly, China is among the top four countries, in
front of the United Kingdom and France. One of the most
active companies regarding patenting has been Incyte
Genomics in the USA. Finland is clearly lagging behind in
patenting. Compared with the high-level research per-
formed, the relatively large number of companies in bio-
technology and their turnover figures, the Finnish activity
in patenting is less than expected and less than that in some
of Finland’s neighbours. It should also be borne in mind
that a keen focus on intellectual property rights (IPR) is one
of the prerequisites for building a globally competitive bio-
technology business.
As the field is young and developing rapidly, the rate of
seeking IPR protection will probably be maintained at least
at the current level for some time. It will be important, in
order to fully exploit the unmet needs, to pay particular at-
tention to IPR issues at an early stage of new technology
development.
19
Proteomic-related patent applications
0
50
100
150
200
250
300
350
400
450
1995 1996 1997 1998 1999 2000 2001
year
Noofapplications
Figure 11. Numbers of proteomics-related patent applications per year.
SOURCE: VTT Technical Research Centre of Finland, Information services
26. 20
0 100 200 300 400 500 600 700
Switzerland
Denmark
Spain
Netherlands
Israel
Italy
Canada
Australia
Sweden
PCT petition
European patent office
Korea
France
United Kingdom
China
Germany
Japan
USA
No of applications
Proteomic-related patent applications by country
Figure 12. Countries where proteomics-related patents have been filed.
SOURCE: VTT Technical Research Centre of Finland, Information services
27. Current capabilities in Finland
Public service providers
There are two protein chemistry laboratories at the Univer-
sity of Helsinki: one at the Institute of Biotechnology on
the Viikki Campus and one at Biomedicum Helsinki. The
Protein Chemistry Laboratory in Viikki is more a research
facility than a core unit, focusing on protein separation and
sample handling techniques. The Laboratory has nanoLC +
Q/TOF and MALDI-TOF/TOF — the only one in Finland.
New LC equipment acquired in the autumn of 2003 allows
2D-LC fractionation on proteomics scale. In Viikki, there
were no further plans in 2003 for robotics or high through-
put systems. The Protein Chemistry Laboratory staff con-
sist of the head of laboratory, a technician, a student and a
researcher. Only the head of the laboratory has a faculty
position, other staff are on project-based contracts. The
Laboratory provides services not only to the Viikki re-
search groups but also to some, mainly Finnish companies.
The Biomedicum Proteomics Laboratory now has a diges-
tion robot, almost new MALDI-TOF and a new IT with
autosampler-nanoLC equipped with a MALDI-plate frac-
tion collector. The Laboratory is interested in developing
clinical applications and also in participating in the devel-
opment of new technology. The Laboratory is a core facil-
ity, and the head and one technician therefore have faculty
positions; researchers are remunerated from various pro-
jects funds.
Oulu has a relatively new facility with a very strong 2D
side, including an Amersham Bioscience DALT system,
which allows ten gels to be run simultaneously, a good se-
lection of analysis software and good MS instruments
(Q/TOF and MALDI-TOF). The only shortcoming is the
lack of nanoLC. Nevertheless, the facility has plans to ac-
quire LC and then a robotics system. To begin with, the fa-
cility will analyse samples from within Biocenter Oulu, but
later on, joint projects with industry will be on the agenda.
The facility employs two post-doctoral researchers and one
technician.
Major Finnish university centres are included in the list in
Appendix 1. At the University of Kuopio, each department
performing 2D GE has its own 2D equipment and software.
Autosampler-nanoLC + IT MS and old MALDI-TOF in-
struments are located in separate departments. IT is used
only partly for proteomics and mostly for pharmaceutical
chemistry. With proteomics continuously increasing in
popularity, new equipment will also be needed at the Uni-
versity of Kuopio. As it is, some university research groups
purchase analyses from Turku and Helsinki. New equip-
ment has been evaluated, and there are inter-departmental
efforts to acquire more instrumentation suitable for
proteomics.
In Turku, the proteomics core facility is located at the
Turku Centre for Biotechnology (TCB), which serves re-
searchers at both the University of Turku and Åbo
Akademi University. The proteomics unit has MALDI-
TOF and autosampler-nanoLC + Q/TOF and, since the au-
tumn of 2003, also a digestion robot. The plan is to increase
throughput but also focus on protein separation techniques.
New instrumentation is needed — such as 2D-LC and
MALDI-TOF/TOF — for more effective protein studies.
At the unit, fulltime staff include a director, one half-time
technician and two researches. VTT is planning to develop
this resource in collaboration with TCB. This would also
fulfil the proteomics needs of the newly established Medi-
cal Biotechnology unit of VTT.
VTT Biotechnology at Espoo also has proteomics activi-
ties without suitable MS equipment of its own, and protein
analysis is therefore done by collaborating with other cen-
tres. The 2D side is strong, including a DALT system and
the second Progenesis software licence in Finland (the
other one is in Oulu). Because of the need for higher
throughput proteomics than available today, VTT is plan-
ning to develop this resource in collaboration with TCB.
This would also fulfil the proteomics needs of the newly
established Medical Biotechnology unit of VTT.
Needs expressed by companies
In the interviews with representatives of Finnish industry,
several issues emerged as important (Table 4). Reliability,
quality of results and sensitivity of analysis were found to
be most important technological attributes. They were met
to a great extent, but not to the level desired. Protein identi-
fication, PTM analysis and functional studies were among
the needs expressed by the companies. Of these, the need
for functional studies, was met to the lowest extent, to-
gether with quantification and throughput.
21
28. For the future, addressing the quality of results, sensitivity
and costs was considered most important. The quality sys-
tem applied by the service provider is most importance to
industrial customers. This was brought up in many inter-
views, and there is need for improvement at present. PTM
analysis, protein functional studies and search for new
biomarkers were among the most important research topics
requiring added attention.
Conclusions
In Finland, the proteomics research effort is younger than
in Denmark or Sweden, for instance, not to mention the
USA or Germany. As evidenced by the numbers of publi-
cations and patent applications, many countries have also
entered the proteomics field much more energetically than
Finland. If Finland’s proportion of the world activity in
proteomics is maintained at the current, low level, the po-
tential positive impacts of modern proteomics methods on
the Finnish biotechnology industry will not be obtained.
This can have long-reaching effects, as new developments
in proteomics are persistently gaining in momentum.
Denmark and Sweden have a longer history in proteomics
research and technology development, and there are some
well-established facilities in these countries. In Sweden,
the building of new proteomics facilities received an addi-
tional boost a few years ago, leading to the establishment of
efficient new facilities in the Lund area. The biotechnology
industry is not the main focus of the new facilities since
their performance is mainly measured in terms of the num-
ber of publications they produce (Appendix 1).
In several other countries, there are full-fledged high-
throughput proteomics facilities. In the USA, many labora-
tories possess more than one piece of identical equipment
dedicated to a particular application, allowing real high-
throughput analyses to be carried out. Compared with Fin-
land, other countries have much higher numbers of staff
working at their proteomics facilities, and the major part of
funding is more long-term by nature than is the case in Fin-
land. Owing to the higher level of investment, many facili-
ties abroad also have the advantage of more expensive in-
strumentation, such as FTICR, over their Finnish counter-
parts.
Limited equipment also restricts the knowledge base and
the extent of results obtainable. Proteomics is heavily in-
strument-oriented because different equipment yields dif-
ferent type of data. A single instrument will not suffice one
intends to carry out high throughput analysis, analyse a
wide range of PTMs, fragment whole protein, obtain the
accurate mass of intact proteins, perform high-energy col-
lisions and set up chip applications. The most efficient way
22
Issue Importance today Fulfilled today Importance of being
fulfilled in future
Reliability (system stability) ✯✯✯ ✯✯ ✯✯
Quality of results ✯✯✯ ✯✯ ✯✯✯
Sensitivity ✯✯✯ ✯✯ ✯✯✯
Resolution ✯✯✯ ✯✯ ✯✯
Quantification ✯✯ ✯ ✯✯
Throughput ✯✯✯ ✯ ✯✯
Costs ✯✯ ✯✯ ✯✯✯
Ease-of-use ✯✯ ✯✯ ✯✯
Software capabilities ✯✯ ✯✯ ✯✯
Reporting ✯✯ ✯✯ ✯✯
Automation ✯✯ ✯✯ ✯✯
Protein identification ✯✯✯ ✯✯ ✯✯
Protein interaction studies ✯✯ ✯✯ ✯✯
Post-translational modifications ✯✯ ✯✯ ✯✯
Protein profiling ✯✯ ✯✯ ✯✯
Functional studies ✯✯ ✯ ✯✯
Search for new biomarkers ✯✯ ✯✯ ✯✯✯
Table 4. Importance of various issues queried in interviews. The number of ✯s indicate importance or
degree of fulfilment. Items in bold: see text.
29. to do serious proteomics research and perform detailed
protein studies is to have access to a variety of MS instru-
ments, with which to approach the same biological re-
search problem from different angles. Information sharing
among core facilities should be encouraged.
Phage display technology and other binder library technol-
ogies represent a so far underexploited resource in proteo-
mics. In Finland, phage display can contribute to develop-
ing relevant contents for protein arrays. The technology is
well established and used mostly for identification of spe-
cific protein binders for diagnostics and drug development.
The size of the libraries (potentially 1—100 billion differ-
ent binders) makes them an ideal tool for various screen-
ing. Not only various proteins but even PTMs and protein
complexes can be analysed with high-capacity array tech-
nologies. Furthermore, these technologies are not limited
to static analysis, but are well suited for functional proteo-
mics, too. The intellectual property (IP) issues related to
the above technologies deserve more detailed analysis, but
as a whole, the freedom to operate is greater in Finland than
in many of other European countries. In addition, the recent
court rulings in the USA would appear to improve rather
than decrease the business potentials of offering analytical
services in third countries where patents on these technolo-
gies have not been filed.
The education issue should also not be overlooked. At
present, regular university training teaches little about the
basics of protein handling. This also concerns instrumenta-
tion, particularly mass spectrometry, where better basic ed-
ucation is needed. In Finland, the practical ‘hands-on’
learning could be provided on collaborative courses ar-
ranged by the core facilities. This would also contribute to
knowledge sharing among the centres.
In Finland, potential synergies have not been fully ex-
ploited in the discipline of proteomics. One way to accom-
plish this would be to create an association or other type of
a forum where experiences and new technology develop-
ments could be shared. The survey conducted for this re-
port revealed that there was very little collaboration among
the Finnish proteomics core facilities. In some cases, even
basic knowledge of each other was missing. On the other
hand, the fact that no major investment, such as in Sweden,
has been made in proteomics facilities and other infrastruc-
ture could constitute an incentive to building a bigger
knowledge base through both domestic and international
collaboration.
23
30. Conclusions
Market
The proteomics analysis market has grown rapidly in the
past few years and is expected grow at a double-digit rate
for some years to come. This is due to an increased demand
for analyses both within academic research and in industry.
The purchase plans of Finnish proteomics facilities include
items such as:
• 2D and LC sample separation technologies
• MS instrumentation
• Software.
Additionally, as the knowledge about basic cellular path-
ways increases, the demand not only for high throughput
proteomics analysis but also for more precise analysis will
increase. In disease predisposition studies, theranostics in-
cluding drug efficacy and early ADME-TOX profiling,
proteome analysis is yet to be fully exploited. Diseases in
Western populations, such as various cancers, are some of
the areas where the modern technologies will be first used.
As a whole, drug development and clinical proteomics pro-
filing will be driving the markets during the next years. In
the biotechnology industry, proteomics coupled to meta-
bolic engineering will improve the competitiveness of the
industry, leading to more effective products and more effi-
cient processes.
Technology
As long as sample preparation is done well, and the
genomic sequence of the organism in question is available,
proteome analysis is straightforward. In many cases, how-
ever, this is not the situation, and problems may occur.
There is still a need to simplify the analytical process to
make it more robust, rapid and reproducible. This is partic-
ularly important with regard to protein identification, as so
far only a few tens of percent of human proteins have been
annotated and identified. Furthermore, once PTMs with
peptide sequences need to be analysed, the throughput
drops dramatically. Today, these complex analyses are
mainly performed at established proteomics centres (Ap-
pendix 1).
Although the use of gel-based separation is expected to
grow, main developments are probably going to take place
in LC/LC-MS/MS technologies. If the procedure can be re-
liably standardised with adequate data handling, process-
ing of LC/LC-MS/MS spectra and identification of pro-
teins from large data sets can be automated much further
than seen today.
Protein chips are an interesting technology platform for fu-
ture products. As of today, their main use is in expression
studies using arrays of thousands or tens of thousands of
spots. In these systems, however, sensitivity is an issue
(there being available for proteins no equivalent to the
polymerase chain reaction of DNA), the small spots may
contain too small amounts of proteins of interest, or there
may be no suitable detection agents. In addition, if antibod-
ies are used either as specific collecting compounds or for
detection, their specificity and stability are additional fac-
tors with strong effects on the outcome of protein chip
analyses. In conclusion, protein chips are starting to find
use in the search for more precise clinical markers in vari-
ous cancers [2] and in research on cellular pathways. To-
day, the lack of large-scale content is still a major obstacle.
There are a number of efforts underway to generate
well-characterised antibodies and proteins to cover the
products of all human genes. These projects are planned to
be completed in a few years time. Once ready, there will be
chip content sources for constructing various protein chip
formats to those applications where they can be used to the
greatest benefit.
Applications
The applications of proteomics include research into new
bioactive molecules, as well as uses related to process de-
velopment and quality assurance (QA). The identification
of proteomic profiles for diagnostics, prediction of thera-
peutic outcomes and drug target validation is gaining much
attention. Other current and presumably growing targets
for proteomics include protein engineering and biotechno-
logical process development (Table 5).
The systems biology era will set new standards for data in-
tegrity, handling and analysis. Proteomics data will be a
cornerstone in understanding biological processes in health
and disease.
25
31. Diagnostics
One of the fastest growing application areas for diagnostics
is the discovery and identification of individual differen-
tially expressed proteins in biosamples [18]. Proteomics
has proved valuable specially in the research on novel se-
rum biomarkers in cancer. Preliminary reports on serum
protein profiling studies indicate that more precise diagno-
ses can be obtained if the decision is based not only on one
or two markers but on a whole set of defined markers.
Therapeutics
Biomarker identification serves both diagnostics and drug
development. Proteomics can be used for target identifica-
tion and validation. In addition to profiling known drugs,
proteome analysis can produce predictive profiles of new
lead molecules for use in ADME-TOX analysis and subse-
quent clinical trial phases. As expression array data start to
be used to support the theranostics approach and, in the
longer term, for personalised medicine, proteomics can
certainly be considered as a value-adding factor in the era
of the new health-care paradigm.
Biotechnology industry
Proteomic analysis, coupled to systems biology informa-
tion, is an important modern tool to improve microbial pro-
cesses and products. This is also true for the diagnostics
and pharmaceutical industries, where proteomics methods
can be applied to process enhancement, QA and trouble
shooting. Ever greater numbers of basic industrial and con-
sumer products are made using microorganisms, with
proteomics playing a central role in providing tools for ge-
netic engineering and process optimisation.
26
Industry Applications
Drug development Target identification
Target validation
ADME-TOX profiling
Product development and process QA
Diagnostics Diagnostic profiling
New biomarkers
Product development and process QA
Bioindustry Metabolic engineering
Product development and process QA
Food Protein profiles, effects of functional foods
Product development and process QA
Table 5. Potential applications of proteomics.
Applications today Services available Potentials Improvements needed in service
Drug development XS S L Quality system
Diagnostics S S L Quality system
Serum sample handling
Bioindustry S M L Throughput
Sequence data annotation
Food XS S M Sample treatment processes
XS = very small, S = small, M = medium, L = large
Table 6. Impact of proteomics today.
32. Recommendations
• Finland is lagging behind Nordic and other European
countries in proteomics-related research and IPR
• Investment in proteomics infrastructure and
staffing needed
• Potentials and services in proteomics are not widely
known
• Biotechnology industry could benefit more from
proteomics
• Opportunity for novel biomarkers
• Opportunity for new technology development.
In Finland, the funding base for innovative and challenging
technology development programmes, such as those re-
quired in proteomics, is weak compared with major com-
petitors, e.g. Sweden and Denmark. Proteomics is much
more expensive than and not as easy to automate as
genomics. Funding for strategic basic technology develop-
ment needs to be increased in Finland.
⇒ The current Infrastructure Programme of the Academy
of Finland is well placed to start to address this issue
⇒ Apply for funding for next-generation proteomics
technology platforms
Collaboration and resource coordination should be im-
proved in and among Finnish proteomics core facilities. In-
vestments have so far been directed to instrumentation,
whereas most of the staff are on temporary project con-
tracts. This makes it difficult to systematically train skilled
researchers who could utilise the investments to full advan-
tage. In a country such as Finland, the knowledge available
should be more readily communicated among the core fa-
cilities, not only to fully exploit the potentials in research
but also to exploit these in industry. There is expertise in
various areas, and obviously the most efficient way for-
ward is to utilise the most experienced forces available for
addressing any particular problem. Collaboration with in-
ternational core facilities should be developed further.
⇒ Arrange seminars and/or symposia to discuss current
issues and future actions
⇒ Start Finnish Proteomic Forum
⇒ Concentrate special technological skills at appropriate
locations, i.e. build ‘distributed critical mass’
The web survey for this report confirmed the general lack
of knowledge about the services available. Nevertheless,
almost all of the respondents expressed a firm interest to
exploit the potentials once these are recognised and the ser-
vices are readily available. As mentioned above, the ex-
ploitation of novel biomarkers in drug development, diag-
nostics and, eventually, theranostics represents a still
mostly unused resource to improve the competitiveness of
Finnish industry. So far, Finnish industry is not fully aware
of the potentials offered by proteomics.
⇒ Implement one-door service: “Need proteomics?
These are the service providers; please contact
Mr/Ms/Mrs…”
Pricing of services is an important aspect of the proteomics
sector. All of the facilities surveyed (whether in Finland or
abroad) had differential pricing for academic and industrial
accounts. The pricing for academics is subsidised, based in
part on the scientific goals set for the facilities and only in
part on the actual costs of producing the services. In the
case of straightforward analyses, present technologies al-
low a positive cash flow to be generated. Pricing may be
problematic, however, whenever the complexity of the
samples calls for a range of different analytical technolo-
gies. Overall, it is currently difficult to operate a profitable
business in proteomics analysis.
⇒ Develop a virtual proteomics centre, optimising usage
of investments and resources
⇒ The centre should have a quality system accepted by
industrial customers
Finland has a strong diagnostics industry which so far has
focused on developing specific assays for individual pro-
teins. As the knowledge about proteomic profiles and pat-
terns increases, particularly with regard to complex dis-
eases, this knowledge can be used for better diagnostics
and better prediction of therapeutic outcomes. Tekes to-
gether with Finnish industry is keen to encourage the effec-
tive utilisation of the existing resources, academic groups
and core facilities for the development of future diagnos-
tics and therapeutics. Proteomics research may uncover
new biomarkers for personalised medicine. This together
with valuable clinical sample materials from completed,
on-going and planned clinical trials, forms a highly com-
petitive, largely unused asset. The existing expertise in
genomics and its translation into proteomics skills should
be explored.
⇒ Develop the immunoproteomics concept further
⇒ Focus on clinical areas, where need, samples and
knowledge exists
⇒ Bring together the Finnish binding library expertise
and reagent business expertise
27
33. The strong Finnish tradition in instrument, reagent and sys-
tem development should be utilised to create technology
platforms for next-generation proteomics. The new busi-
ness potentials in next-generation proteomics are related to
a smooth integration of instrumentation and software. The
demanding multi-disciplinary effort, including micro-
arrays, microfluidistics, nanotechnology, etc., should aim
at more automated and robust technology for proteomics
than is available today. This calls for close collaboration
among various disciplines, such as physics, biology, medi-
cine, instrumentation technology and computer science.
⇒ New proteomics platform development, combined
with microfluidistics, bioinformatics and binder
libraries
⇒ Coordinated efforts between systems biology and
bioinformatics programmes
⇒ Combine knowledge in biology/proteomics to that
in information technology
Understanding of the biological phenomena behind dis-
eases would make it possible to tailor treatment schemes
and diagnostics more precisely than is possible today.
NOTE. The above-mentioned applications are not limited
to the medical industry. Other bioindustries, e.g. plant bio-
technology and the development of functional food ingredi-
ents, can benefit from high-quality proteomics services and
proteomics-related technology development programmes. It
would be sensible to utilise the technology leverage in areas
where the product development cycle is shorter than for in-
stance in drug development. That way a faster return of the
investment in new technology development could be ex-
pected.
28
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[9] IMSC Edinburgh 2003, Workshop, Garry Corthals,
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Lindh I., McLafferty F.E. Anal. Chem. 73: 19-22, 2001.
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Companies exploiting proteomics
www.abbottdiagnostics.com
www.astrazeneca.com
www.atheris.ch
www.bayerdiag.com
www.cellzome.com
www.chiron.com
www.Digene.com
www.incyte.com
Instrument vendors
www.advion.com
www.agilent.com
www.appliedbiosystems.com
www.bdal.com
www.ionics.ca
www.mds-sciex.com
www.packardinst.com
www.perkinelmer.com
www.shimadzu-biotech.net
www.thermo.com
www.waters.com
Miscellaneous proteomics products
www.amershambioscience.com
www.genomicsolutions.com
www.probes.com
www.proxeon.com
Protein chips
www.affibody.com
www.affymetrix.com
www.bdbiosciences.com
www.biochem.roche.com
www.cambridgeantibody.com/
www.ciphergen.com
www.clontech.com
www.geneprot.com
www.morphosys.com
www.procognia.com
www.prolinx.com
www.sigmaaldrich.com
www.somalogic.com
www.zeptosens.com
www.zyomyx.com
29
36. Acknowledgements
All the researchers and industrial partners participating in the interviews are gratefully acknowl-
edged. The valuable comments received from Professor Olli Kallioniemi, Dr. Matej Oresic and Dr.
Richard Fagerström are also greatly appreciated, as are the productive discussions with Kalevi
Heinola of Tekes during the preparation of the report. Jyrki Äikäs, Dr. Marko Kallio and Professor
David Goodlett provided assistance with illustrations.
31
37. 33
Centre Edman deg. 2D gel runs in-gel digestion MALDI/TOF LC-MS/MS*)
LC-MS/MS#) sample prep+ID: MALDI(/ MS/MS)
1 - x x (auto) x - x N/A
2 x - 85 50 400 incl. ID - N/A
3 - 260 (4 gels) N/A 150 (incl. ID) 250 w/o LC - 250 (500)
4 x x x x x (no LC) -
5 - 111-222(DIGE 444) 2.3 (auto) 22 444 444 244 of 96 samples (+444/sample w/o ID)
6 x - 44.25 55.3 442.3 331.70(+221.15)
7 - 66-82(DIGE181-224) x(auto) 6 -8 - 12-16 2761-5436 (7679-9492) incl. 2D
8 - x x (auto) x x - N/A
9 - x x x x N/A
10 N/A x (auto) x N/A N/A collaboration-based
11 - x (DIGE) x (auto) x x - N/A
12 x x x (‘semi’auto) x - - N/A
13 - x (DIGE) x(auto) x x(FTMS) x N/A
14 - x (DIGE) x (auto) x x x N/A
15 - - - (ICAT) x x (also MALDI-) x N/A
16 - - N/A - - x 259-345
*) High-resolution MS equipment #) Low-resolution MS equipment
CENTRES: ADDITIONAL INFORMATION:
1 Biomedicum, Protein Chemistry Core Facility Also microfluidistics
2 University of Helsinki, Institute of Biotechnology MALDI-TOF/TOF
3 Turku Centre of Biotechnology ICAT in use (only one in Finland)
4 Biocenter Oulu, Protein Analysis Core Facility Strong 2D know-how, many different analysis software. No LC in MS/MS system
5 Lund Proteomics Resource Centre Fully automatic, in-gel digestion is charged always as 96 or x*96. Advion ESIchip in use
6 Karolinska Institut, protein analysis center No specific information available about LC-MS/MS system, bioinformatics available
7 Russian academy of medical sciences, IBMC Three LC-MS/MS equipment, also MALDI-TOF/TOF and SELDI. Offers 2D courses.
8 EMBL, proteomics visitor facility Commercially sponsored facility, special multiprocessor searches
9 Functional Genomics Center of Zürich Provides teaching
10 The University of Liverpool, Human anatomy and cell biology
11 Cambridge Centre of Proteomics Only to Drosophila and Arabidopsis community
12 Edinburgh Protein Interaction Centre Bioinformatics available as ‘biocomputing’
13 Scripps Institute Includes practically all one can imagine in the field of proteomics, many MS equip.
14 Vanderbilt university, MS/Proteomics Core facility Protein profiling from tissues, fully auto (LIMS), many different MSs, MALDI-TOF/TOF
15 Institute of Systems Biology, HTP Proteomics MALDI-TOF/TOF and -QIT/TOF, many different (and same) MSs
16 Harvard Medical School, MS facility Only LC-MS/MS (three of them) available, phosphorylation analysis carried out
Appendix 1 Equipment, services and rates of selected proteomics centres
Prices/sample (in euros) are those for research community in year 2003. Prices for outside research institutes (non-commercial) are usually twice these amounts.
The dashed lines separate geographic areas.
38. Appendix 2
Examples of companies and organisations interviewed for the survey
34
Company Line of business Comments
Agilent Technologies Inc LC/MS/software supplier Techn. development/applications
Amersham Biosciences LC/MS/reagent supplier Automation, MS, labels
Astra Zeneca Pharma company Drug development
Biogenon Oy Protein arrays Start-up/technical development
Bruker Daltonics MS systems Technical development
Finnish Red Cross Blood Service Blood-derived products
Geneos Oy Asthma/allergy diagnostics Genetic screening
Hormos Medical Oy Drug development Small pharma company
Hytest Oy Diagnostics OEM provider
Innotrac Diagnostics Oy POC1
Diagnostics System development, biomarkers
Juvantia Pharma Ltd Drug development Small pharma company
Medicel Oy Research in systems biology Yeast as model
Orion Pharma Oy Drug development Own proteomics facility
Orion Diagnostica Oy POC diagnostics New biomarkers
PerkinElmer LS, Wallac Diagnostics/Pharma Diagn. systems/screening techn.
VTT Biotechnology research Service provider, techn. devel.
1
POC = point of care
Note. The above include organisations responding to the web survey.
39. 35
Company Name of product Array Capability Detection
1 BD Clonetech Antibody Microarray 380 Antibody array, covalently immobilised on glass slide 378 membrane and cytosolic
proteins
Detection of labelled sample
2 U-c Fingerprint Lectin-based glycan microarray platform - Labelled probes
3 Panorama Antibody Microarray cell
signalling kit
Antibody array, nitrocellulose-immobilised 224 antibodies to key cellular
proteins
Detection of labelled sample
4 Zyomyx Human Cytokine Expression
profiling assay
Special chip technology Allows 30 cytokines to be
profiled
Fluorescence
5 SELDI Different surface types, hydrophobic, ion exch., antibody - TOF and Q/TOF MS
6 ZeptoMARK Very sensitive platform 6 000 immobilised recognition
elements
Labels with planar waveguide
7 Versalinx Immobilisation platform (phenyldiboracic acid and
salicylhydroxamic acid)
As you wish
8 - Photoaptamer arrays for research and clinical use - Fluorescence staining of bound
proteins
9 - Affibody molecules replace antibodies in array 10e5-10e10 different affibody
molecules
As you wish
10 - Produces monoclonal human antibodies with phage display Libraries of antibody genes (over
100 billion)
As you wish
11 HuCAL Produces human antibodies by a special technique Extensive libraries As you wish
12 Yeast ProtoArray
product pipeline Offers ready and addressed arrays, patented ProtoP5
allows rapid production of purified proteins
In Yeast ProtoArray
, almost
5 000 spots duplicated on a
slide
Flexible
Appendix 3
Protein chip-related companies
Ready chips Platforms Array content providers ‘Full service’
1 BD Biosciences 5 Ciphergen 9 Affibody 12 Protometrix
2 Procognia 6 ZeptoSens 10 Cambridge Antibody Technologies
3 Sigma-Aldrich 7 Prolinx 11 Morphosys
4 Zyomyx 8 SomaLogic
40. Technology Reviews of Tekes
36
157/2004 Proteomics – Challenges and possibilities in Finland. Heini Koivistoinen, Harri Siitari. 35 p.
156/2004 Finnish Software Product Business: Results from the National Software Industry Survey 2003.
Juhana Hietala.
155/2004 Globaali tietoyhteiskunta – Kehityssuuntia Piilaaksosta Singaporeen. Pekka Himanen (toim.).
114 s.
154/2004 Logistiikan sähköisten tieto- ja viestintäteknologioiden hyödyntäminen – Kokemuksia suoma-
laisista yrityksistä. Jouni Kauremaa, Jaana Auramo. 49 s.
153/2004 Ravitsemushoidon kustannusvaikuttavuus – taloudellinen arviointi kansansairauksien
ehkäisyssä ja/tai hoidossa. Anne-Mari Ottelin. 37 s.
152/2004 Viranomaisvalvonta kudosteknologian tuotekehityksessä.
151/2004 Toimialakehitys ohjelmistoteollisuuden vauhdittajana – Uutta liiketoimintaa lähialoilta.
Pasi Tyrväinen, Juhani Warsta, Veikko Seppänen. 71 s.
150/2003 Towards a Supercluster: Chemical and Biochemical Innovations Connecting Finnish Clusters.
149/2003 Managing Non-Core Technologies: Experiences from Finnish, Swedish and US Corporations
Annaleena Parhankangas, Päivi Holmlund, Turkka Kuusisto. 76 p.
148/2003 Kantasolutoimiala Suomessa. Toimijoiden näkemyksiä vuonna 2003. Noin 90 s.
147/2003 Innovative waste management products – European market survey. Christoph Genter. 40 p.
146/2003 Elektroniikan lämmönhallinta. Simo Keskinen. 8 s.
145/2003 Meriklusterikatsauksen englanninkielinen versio.
144/2003 Tracing Knowledge Flows in the Finnish Innovation System – A Study of US Patents Granted
to Finnish University Researchers. Martin Meyer, Tanja Siniläinen, Jan Timm Utecht,
Olle Persson, Jianzhong Hong. 36 p.
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Mika Vaihekoski, Seppo Leminen, Joonas Pekkanen, Jussi Tiilikka
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137/2003 Kohti kansainvälistä arvoverkottunutta rakentamista - Linjaukset rakennusklusterin teknologia-
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