MetaboScape
All-in-one software for compound identification from non-targeted workflows
Identify more with MetaboScape
Add confidence to your IDs using annotation quality (AQ) scoring with CCS. Visualize biomarkers using built-in statistical tools and map changing pathways.
Utilize the 4th dimension using TIMS to reveal CCS for all your compounds
Process large sample cohorts rapidly using MetaboScape’s client-server-based software. Run > 200 samples per day using LC-free MRMS aXelerate.
Annotate imaging data with compound information, whilst detecting more compound classes using the innovative and unique MALDI-2 source on the timsTOF fleX.
Prosigna Score / ROR Score:
The ROR Score has been validated to predict the risk of recurrence of disease in ER+ breast cancer after surgery and treatment with 5 years of endocrine therapy. The ROR score depends upon the biology of the intrinsic subtypes, the proliferation score of the tumor, and the tumor size as shown in the equation below:
ROR = aRLumA + bRLumB + cRHer2 + dRBasal + eP + fT
Each of the R variables in the equation above indicate the Pearson correlation coefficient of the PAM50 expression profile for the tumor compared to each of the prototypical centroids for the intrinsic subtypes shown in the heatmap below. P is the proliferation score, which is the average gene expression profile of genes associated with cell-cycle progression and T is the tumor stage.
Figure: Heatmap of PAM50 genes by subtype. Red is higher expression and green is lower expression
GeoMx DSP COVID-19 Protein and RNA Analysis
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Rapidly perform high-plex spatial analyses of the host response in FFPE or fresh frozen tissue using the GeoMx Digital Spatial Profiler (DSP). NanoString’s GeoMx DSP platform enables high-plex protein and RNA experiments in key areas of biology such as molecular response, cellular (immune) response, tissue damage, and drivers of individual susceptibility to severe forms of disease.
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The GeoMx COVID-19 Immune Response Atlas, a ~1,850-plex RNA assay, enables spatial studies of the SARS-CoV-2 virus and host response. RNA targets include COVID-19 receptors and proteases, pulmonary alveolar type I and II markers, lung biology markers, viral response markers, and SARS-CoV-2 probes. RNA targets are profiled simultaneously using the GeoMx DSP and an Illumina next-generation sequencer (NGS) for readout. Users can run ACD RNAscope™ probes alongside GeoMx RNA probes to identify regions of interest.
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A five-antibody custom, ready-to-go protein panel, with receptor, protease, and viral markers is available through the GeoMx Technology Access Program or for order through Abcam. This COVID-19 GeoMx-formatted Antibody is run with the 20-plex GeoMx Immune Cell Profiling Core (plus controls) with readout on the nCounter Analysis System. Users can add up to six 10-plex modules including the Immune Activation Status, Immune Cell Typing, and/or Cell Death modules to more deeply profile proteins involved in T cell activation and cell death. NanoString scientists can recommend commercially-available markers for lung epithelium, nasal epithelium, immune response markers, and the viral spike protein.
AUTOIMMUNE DISEASE AND CHRONIC INFLAMMATORY DISEASE COVERAGE
Condition
Description
Chronic inflammatory disorder that impacts the lining of joints.
Chronic inflammatory of the digestive tract.
Autoimmune disease is where the immune system mistakenly attacks the insulin-producing cells of the pancreas
Demyelinating disease that disrupts communication with the nervous system.
Immune-mediated disease that causes skin cells to rapidly build up on the surface of the skin
Certain treatments and infections have been reported to interfere with the immune system and induce a series of autoimmune disease or adverse immune-related events.
Chronic inflammatory disease that manifests systematically throughout the body.
Rheumatoid Arthritis
Inflammatory Bowel Disease
Type 1 Diab
Type 1 Diabetes
Multiple Sclerosis
Systematic Lupus Erythematosus
Psoriasis
Induced Adverse Immune Events
Immune Checkpoint Coverage
ADORA2A(A2aR)
CD70
HAVCR2(TIM3)
CD274(PD-L1)
TNFRSF9(4-1BB)
TNFSF9(4-1BBL)
TNFRSF18(GITR)
TNFSF18(GITRL)
VSIR(VISTA)
PDCD1LG2(PD-L2)
TIGIT
TNFRSF4(OX40)
TNFSF4(OX40L)
ICOS
ICOSLG(B7-H2)
LAG3
PDCD1(PD-1)
CD80
CD86
CD276(B7-H3)
CTLA-4
CD27
CD28
CD40
CD40LG
Functional Annotations
Pathways Regulating Glia
(178/180 Hs/Mm Genes)
Inflammation & Peripheral Immune Invasion
(187/188 Hs/Mm Genes)
Cell Stress & Damage Response
(127/134 Hs/Mm Genes)
Angiogenesis
Apoptosis
Autophagy
Cell Cycle
Hypoxia
NO Metabolism and Signaling
Oxidative & Nitrosative Stress
Proteotoxic Stress
Calcium Signaling
Circadian Signaling
Ion Transport
JAK-STAT
Lipid Metabolism
MAPK & PI3K
TGF-Beta Signaling
Wnt Signaling
Antigen Processing & Presentation
Cell Migration
Chemokines
Complement System
Cytokines
Inflammasome
Interferon Signaling
NK-kappaB Signaling
Phagocytosis
T-Cell Signaling
Powerful T-ReXalgorithm
MetaboScape®’s powerful T-ReXalgorithm comprises retention time alignment, deisotoping, and feature extraction to ensure robust data processing
User-defined Analyte Lists
Target compounds can be automatically annotated using user-defined Analyte Lists
Unknown ID
Unknown ID pipeline including library matching and in silico fragmentation to facilitate unknown ID
Visualize Relevant Information
Visualize relevant information in complex data sets using supervised and non-supervised statistics, including PCA, t-test, ANOVA, PLS, and bucket correlation analyses
Annotation Quality (AQ)
Annotation Quality (AQ) scoring providing five indicators of data quality
Pathway Mapping
Pathway mapping to set identified metabolites in a biological context, thereby turning data into knowledge
Local Metabolite Prediction
Identification of drug and xenobiotic metabolites using local metabolite prediction
Batch Corrections
Batch correction to offset sample effects in large sample cohorts
Investigate Changes
Time series plots to investigate changes in metabolites over time
Lipidomics Annotation Tools
Dedicated lipidomics annotation tools, including rule-based annotation, 4D Kendrick mass defect plot and CCSPredict
Features
The eight essential components of stem cell biology
Stemness
Pluripotency
Regulatory Signaling
Epigenetics
Mechano-Signaling
Metabolism
Differentiation Signaling
Lineage Specification
Stem Cell Renewal:
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Stem Cell Prolifiration
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Cell Cycle
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Senescence/Quiescence
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Autophagy
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Apoptosis
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Anti-Apoptosis
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PSC Pluripotency Markers and Regulators
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Naive State/Primed State
Regulatory Pathways:
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Wnt/B-catenin Pathway
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Hedgehog Signaling
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AP-1 Signaling
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PI3K-AKTmTOR Pathway
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MAPK Pathway
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JAK/STAT Pathway
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Notch Signaling
Epigenetic Mechanism:
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DNA Methylation
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Histone Acetylation & Methylation
Mechano-Signaling:
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Rho/ROCK Signaling
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integrin/Cadherin Signaling
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Hippo Pathway
Metabolism:
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Oxidative Stress Response
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Hypoxia Response
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Amino Acid Metabolism
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Fatty Acid Metabolism
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Glutamine Metabolism
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Glucose Metabolism
Differentiation Signaling and Pathways:
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TGFB Signaling
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Cytoskeletal Reorganization
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MET/EMT Signaling
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HOX Gene Activation
Differentiation Lineage:
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Endodermal /Ectodermal /Mesodermal Lineage Markers
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Key Somatic Cell Types
Custom & Clinical Products
Assay Type
Product
Maximum Targets
Daily Sample Throughput
Analytes Offered
Common Applications
Custom codeSets
Elements TagSets
PlexSet Reagents
Self-assembled, interchangeable probes, optimized for smaller validation projects with maximum flexibility
Self-assembled, interchangeable probes for high-throughput, sample multiplexing projects
User-designed, turn-key solution that comes ready-to-use
216
96
800
24-96
24-96
192-1152
mRNA, CNV, Fusions
mRNA, Fusions
mRNA, miRNA, CNV, Fusions
Cell line drug screen, biomarker development, infectious disease
Gene Signature Development
Model Organism, Microbes, Agriculture
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