Protein Profiling Platform - Quality Assurance

High quality standards are essential for robust and reliable Biomarker Discovery and Verification as well as for the discovery of new Drug Targets. During the last 10 years a stringent quality assurance workflow has been established for our Antibody Array Platform in order to conduct immuno-based biomedical discovery studies with excellent standards in terms of reproducibility and platform stability. The automated assay workflow further improves the performance of our service. 

 

Biomarker Discovery Phase - scioDiscover Platform

  • Stringent antigen design for maximised specificity of the resulting antibodies
  • Antibodies are antigen affinity-purified
  • Targets identified through transcriptional studies and expert input
  • Stringent QC management
  • Features:  
    • cross-species activity (human and mouse for high versatility)
    • detection of several protein isoforms
    • cost-efficiency through high content

  

Verification Phase - Custom Array Platform

  • Stringent antigen design for maximised specificity of the resulting antibodies
  • Antibodies are antigen affinity-purified
  • In-house QC on Western Blot (different cell lines or tissues) and optional ELISA-based tests
  • In-house QC on large-scale protein arrays (> 9.000 human proteins)
  • In-depth validation of array performance
  • Definition of biomarker signature with highest accuracy
  • Selection of appropriate binders / sandwich pairs
  • Features:  
    • specifically designed antibodies for further use in diagnostic assays
    • fully renewable antibody formats
    • in-depth quality controlled (WB, ELISA)
    • comprehensive cross-reactivity profile (large-scale protein arrays)

 

Orthogonal Biomarker Validation

Verified Candidates can be further validated by orthogonal methods according to customer’s requirements

  • Western Blotting ( WB )
  • ELISA
  • Immuno-Precipitation ( IP )
  • Mass spectrometry ( MS )
  • Biacore

 

Overview
Scio-Discover
    Biomarker
Discovery
    Custom Microarrays
for Biomarker Verification
    Contact
us

scioSpot - Microarray Production

Microarrays - tailor-made for you. With more than 10 years of experience, Sciomics is the ideal partner for designing and printing your antibody-, protein-, peptide- or DNA/RNA chips. Benefit from excellent quality manufacturing and a wide choice of microarray support surfaces and coupling-chemistry optimised for your application.

 

Microarrays possible:

 

Key Applications:

  • SNP analysis and genomic biomarkers (DNA arrays)
  • autoantibody profiling (protein and peptide arrays)
  • protein biomarker verification (antibody arrays)
  • protein expression level analysis and in-depth pathway profiling (antibody arrays)
  • highly-parallel affinity molecule characterisation (various array types)

 

Custom modifications available:

  • Surface chemistry
  • Optimised coupling-chemistry for different molecule classes
  • Spot size / diameter
  • Spot density
  • Numbers of replicates
  • Spotting layout
  • Number of subarrays (distinct incubation areas per microarray)

 

Reference customers:

Hutman Diagnostics, Switzerland

Dr. Stéphanie Renaud, University of Lausanne, Switzerland

 

This email address is being protected from spambots. You need JavaScript enabled to view it. for further information and to discuss your custom microarray production.

 

Target proteins

Our scioDiscover and scioPhospho services are based on complex Antibody Microarrays, also called analytical Protein Arrays or Protein Capture Arrays. Within a single experiment 1030 proteins can be profiled in parallel requiring only minimal amounts of sample. The targets proteins were carefully selected over a period of more than 15 years to cover a broad set of different protein classes as well as pathways important in biomedical studies.

Thereby, the protein profiling covers key pathways in various diseases such as cancer, neurological disorders as well as organ failure. Given the wide spectrum of applications and indications the service is ideal for high-content protein expression level analysis from various biological samples. The broad coverage of many important pathways, extracellular and membrane proteins as well as transcription factors, renders scioDiscover a versatile and efficient tool for discovery projects.

Please find below the distribution of the proteins targeted by scioDiscover according their biological processes (Fig.1), their protein classes (Fig.2), their molecular function (Fig.3) as well as their cellular compartment (Fig.4). In addition, pathways covered by scioDiscover are listed in Table 1.

For the pathways TNF signaling, Cell cycle regulation and pathways important in Cancer, Tuberculosis and Huntington's Disease covered targets are depicted in green.

Please contact us for more information regarding targets and pathways covered or to discuss how we can support your study with a highly-parallel protein analysis.

 

Case study - Bladder Cancer

Case study - Acute Kidney Injury

 

Overview
Scio-Discover
    Biomarker
Discovery
    Target
Discovery
    Contact
us

 

 

Classification of target proteins

Biological processes

Protein classes

biological processes covered by protein array analysis

protein classes covered by protein array analysis

Fig. 1: Distribution of target proteins within different biological processes. The majority of the antibodies on the microarray detect proteins involved in cellular or metabolic processes or are involved biological regulation, in a developmental or immune system process or as a response to a stimulus.

Fig. 2: Distribution of target proteins within different protein classes. With scioDiscover 122 signaling molecules, 113 receptors, 109 nucleic acid binding proteins and 71 transcription factors can be analysed in parallel.

Molecular functions

Cellular compartmenrt

molecular functions covered by protein array analysis

 

cellular compartments covered by protein array analysis

 

Fig. 3: Distribution of target proteins within different molecular functions. The majority of proteins on the protein microarrays measures proteins involved in binding or with a catalytic or receptor activity.

Fig. 4: Target proteins classified according their Cellular Compartment.

 
 

Coverage of pathways

Selected Pathwaysno. targets
Inflammation mediated by chemokine and cytokine signaling (P00031)40
Apoptosis signaling (P00006)38
Gonadotropin releasing hormone receptor (P06664)35
CCKR signaling map (P06959)35
Integrin signalling (P00034)29
Angiogenesis (P00005)28
Interleukin signaling (P00036)27
Huntington disease (P00029)26
p53 pathway (P00059)22
T cell activation (P00053)22
B cell activation (P00010)21
Ras Pathway (P04393)18
Wnt signaling (P00057)17
TGF-beta signaling (P00052)17
EGF receptor signaling (P00018)17
Alzheimer disease-presenilin (P00004)15
FAS signaling (P00020)15
FGF signaling (P00021)14
VEGF signaling (P00056)13
Toll receptor signaling (P00054)13
Parkinson disease (P00049)12
PDGF signaling (P00047)12
Insulin / IGF pathway-mitogen activated protein kinase kinase / MAP kinase cascade (P00032)12
Alzheimer disease - amyloid secretase  (P00003)11
p53 pathway feedback loops 2 (P04398)10
Endothelin signaling (P00019)10
Blood coagulation (P00011)10
Plasminogen activating cascade (P00050)9
Cytoskeletal regulation by Rho GTPase (P00016)9
Interferon-gamma signaling (P00035)8
Insulin/IGF pathway-protein kinase B signaling cascade (P00033)8
Ubiquitin proteasome (P00060)7
Transcription regulation by bZIP transcription factor (P00055)7
PI3 kinase (P00048)7
Oxidative stress response (P00046)7
Cadherin signaling (P00012)7
 

 

Highly parallel protein analysis of TNF Signaling

Fig. 5: Proteins in the TNF signalling pathway covered by our protein array are shown in green.

 

 Parallel Analysis of Cell Cycle Proteins by complex antibody arrays

Fig. 6: Cell Cycle Proteins covered by antibody array are depicted in green.

 

 Cancer protein profiling

Fig 7: scioDiscover has a broad coverage of diverse pathways involved in cancer. Proteins in green can be profiled with scioDiscover antibody arrays.

 

 Protein analysis in Huntington's disease

Fig. 8: scioDiscover has a good coverage of proteins involved in various diseases such as Huntington's disease. Proteins analysed in parallel by scioDiscover protein arrays are shown in green

 

Proteins involved in Tuberculosis

Fig. 9: Pathways involved in Tuberculosis are shown. Proteins covered by the scioDiscover service are shown in green.

 

scioCD - Cell surface marker and Cytokine profiling_v2

 

Characterise a certain cell type ?

 

Cell composition in a certain tissue sample ?

 

In-depth profiling of CD-marker expression ?

 

Increase your throughput at high sensitivity levels ?

You aim at high reproducibility ?

 

 

Our scioCD profiling service covers 206 different proteins by monoclonal antibodies:

All these proteins can be analysed in parallel within a single experiment from minute sample amounts. Thereby, scioCD antibody array analysis service is ideally suited to investigate cell composition of tissues or the differentiation status of cultured cells in a highly parallel, fast and robust fashion. In addition, protein distribution in blood samples (plasma / serum) can be analysed efficiently, providing insights in the blood cell composition.

Combining analysis of signalling and cellular receptor proteins provides in-depth insights into signal transduction processes
Proteins profiled in parallel by scioCD antibody microarray and their interactions

scioCD is a complete sample-to-result service for a variety of different sample types. The respective protocols were developed over a period of 15 years and are optimised towards highest possible sensitivity combined with high reproducibility (coefficients of variation below 10%).

 

 

Target
proteins
      Analysis
Service
      Sample
Types
      Product
brochure
      Contact
us

 

 

 

 

Applications

  • profiling of cell differentiation status
  • stem cell differentiation 
  • investigate soluble CD-molecules for e.g. allograft rejection
  • inflammatory response profiling
  • immuno-oncology profiling of check-point inhibitor targets
  • characterisation of tissue-isolated primary cells
  • immune-cell surface marker profiling on
    • various B-cells 
    • stimulated T-cells
    • patient derived T-cells
    • patient derived dendritic cells
  • oncology profiling for new biomarkers e.g. Leukemia
  • tumor micro-environment profiling
  • profile response to stimuli of cell lines
  • evaluate protein expression changes in silencing/overexpression  experiments
 

Advantages

  • high content - 206 proteins are analysed with monoclonal antibodies
  • broad coverage and parallel analysis of
    • 129 CD molecules 
    • 54 cytokines and chemokines
    • 23 other relevant molecules (HLAs, p53)
  • minimal sample requirements
  • native matrixes ( non-fractionated / non-depleted )
  • sensitivity as ELISA or better
  • fully immuno-based assay
  • reliable dual-colour study design
  • high reproducibility, CV < 10%
  • most proteins are covered redundantly by two or more antibodies
  • each antibody is presented in four replicates
  • antibodies are available for follow-up studies


 

Which sample types can be analysed ?

Within our scioCD analysis service the following samples can be analysed:

  • plasma / serum
  • fresh frozen tissue samples
  • cellular content
  • cell culture supernatant
  • cerebrospinal fluid
  • additional sample types on request

  

Sample-to-result service

Within the analysis service, we will not only carry out the microarray experiments but also support you with a suggestion for an appropriate microarray study design as well as with the sample selection process in order to address your scientific question in the optimal way. Within 3-4 weeks after receipt of your samples you will receive a customised study report including a statistical analysis.

Our analysis service includes:

  • definition of an appropriate study design
  • sample preparation
  • protein extraction
  • protein concentration measurements
  • protein quality control
  • sample labelling
  • sample purification
  • incubation of the samples on antibody microarrays
  • microarray scanning
  • raw data acquisition
  • data normalisation
  • data analysis including cluster analysis
  • statistical testing for differentially abundant proteins
  • comprehensive study report

scioSpot - Custom Antibody Microarrays

Antibody Microarrays - tailor-made for you. With more than 10 years of experience, Sciomics is the ideal partner for designing and printing your antibody chips as well as arrays of various affinity molecules such as Nanobodies, scFv fragments or aptamers. Benefit from excellent quality manufacturing and a wide choice of microarray support surfaces and coupling-chemistry optimised for your application.

 

Possible applications:

  • In-depth pathway profiling
  • Profiling of inflammatory markers
  • Profiling of growth factors
  • Investigate toxic and adverse drug effects in animal and cell culture models
  • Parallel Verification of biomarker candidates
  • Development of diagnostic markers
  • Highly-parallel characterisation of large numbers of antibodies
  • Identification of optimal antibodies for ELISA sandwich pairs
  • Longitudinal mouse studies
  • Correlate genomic or transcriptomic data with protein expression data

 

 Key advantages:

  • Highly-parallel protein analysis from the same sample in one experiment
  • High sensitivity (similar to ELISA or better)
  • High reproducibility (CV <13%)
  • Low sample consumption, only 10 ul plasma or serum required
  • Batch sizes from 1 up to 2.000 arrays, low batch-to-batch variation
  • Production is scalable as and when required 
  • Stringent antibody and microarray quality control

 

Reference customers:

Immunotools GmbH, Germany

 

This email address is being protected from spambots. You need JavaScript enabled to view it. to discuss your microarray project. Downlad our flyer for this service here. 

 

 

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