overview radboudumc center for proteomics, glycomics and metabolomics april 2015
TRANSCRIPT
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Translational Metabolic Laboratory Using Proteomics, Glycomics and Metabolomics to translate Research to Biomarkers to Diagnostics
April 2015
Translational Metabolic Laboratory, Department of Laboratory Medicine https://www.radboudumc.nl/Research/ProteomicsMetabolomicsGlycomics/
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Radboudumc • Mission: “To have a significant impact on healthcare” • Strategic focus on Personalized Healthcare through “the
patient as partner” • Core activities:
• Patient care • Research • Education
• 11.000 colleagues • 50 departments • 3.000 students • 1.000 beds • First academic centre outside US to fully implement EPIC
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Patient
Radboud Personalized Healthcare
A significant impact
on healthcare
Molecule
Population
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Personalized Healthcare @ Radboudumc
People are different Stratification by multilevel diagnosis
+ Patient’s preference of treatment
Exchange experiences in care communities Select personalized therapy
Population
Patient
Molecule
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www.radboudumc.nl/research/technologycenters
Genomics
Bioinformatics
Animal studies
Stem cells
Translational neuroscience
Image-guided treatment
Imaging
Microscopy
Biobank
Health economics
Mass Spectrometry
Radboudumc Technology
Centers Investigational
products
Clinical trials
EHR-based research
Statistics
Human physiology
Data stewardship
Molecule
Flow cytometry
March 2015
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Opening Radboud Research Facilities, 2nd Oct 2014
Point of contact: Alain van Gool
About 250 dedicated people working in 18 Technology Centers, ~1600 users (internal, external), ~140 consortia
www.radboudumc.nl/research/technologycenters/
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Genomics
Bioinformatics
Animal studies
Stem cells
Translational neuroscience
Image-guided treatment
Imaging
Microscopy
Biobank
Health economics
Mass Spectrometry
Radboudumc Technology
Centers Investigational
products
Clinical trials
EHR-based research
Statistics
Human physiology
Data stewardship
Molecule
Flow cytometry
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About 250 dedicated people working in 18 Technology Centers, ~1600 users (internal, external), ~140 consortia
www.radboudumc.nl/research/technologycenters/
• Proteins • Metabolites • Drugs • PK-PD
• Preclinical • Clinical
• Behavioural • Preclinical
• Animal facility • Systematic review
• Cell analysis • Sorting
• Pediatric • Adult • Phase 1, 2, 3, 4
• Vaccines • Pharmaceutics • Radio-isotopes • Malaria parasites
• Management • Analysis • Sharing • Cloud computing
• DNA • RNA
• Internal • External
• Early HTA • Evidence-based
surgery • Field lab
• Statistics • Biological • Structural
• Preclinical • Clinical • Economic
viability • Decision
analysis
• Experimental design • Biostatistical advice
• Electronic Health Records • Big Data • Best practice
• In vivo • Functional
diagnostics
• iPSC • Organoids
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Translational medicine @ Radboudumc
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Research Biomarkers Diagnostics
Department of Laboratory Medicine, Radboudumc Integrated Translational Research and Diagnostic Laboratory, 220 fte, yearly budget ~ 28M euro. Close interaction with Dept of Genetics, Pathology and Medical Microbiology
Specialities: • Proteomics, glycomics, metabolomics • Enzymatic assays • Neurochemistry • Cellulair immunotherapy • Immunomonitoring
Areas of disease: • Metabolic diseases • Mitochondrial diseases • Lysosomal /glycosylation disorders • Neuroscience • Nefrology • Iron metabolism • Autoimmunity • Immunodeficiency • Transplantation
In development: • ~500 Biomarkers • Early and late stage • Analytical development • Clinical validation
Assay formats: • Immunoassay • Turbidicity assays • Flow cytometry • DNA sequencing • Mass spectrometry • Experimental human (-ized)
invitro and invivo models for inflammation and immunosuppression
Validated assays*: • ~ 1000 assays • 3.000.000 tests/year
Areas of application: • Personalized healthcare • Diagnosis • Prognosis • Mechanism of disease • Mechanism of drug action
Department of Laboratory Medicine
*CCKL accreditation/RvA/EFI
www.laboratorymedicine.nl
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One genome → multiple proteomes/metabolomes
• The proteomes and metabolomes are the functional output of the genome
• 21.000 genes → approximately 500.000 possible proteins and isoforms and biochemical metabolites
• Proteomes define and reflect the functional state of a cell or organism at a certain time under certain conditions
• Proteomes and metabolome change depending on stimuli and challenges; most cell/tissue signalling occurs through rapid protein changes
• Proteomics and metabolomics are strong approaches to identify and analyse metabolic changes of cell/tissue/organism
• Unique added value of proteomics: • Protein expression • Post-translational modifications • Protein complex formation + function
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One genome → multiple proteomes
Body fluids
Tissues
Cells
Plasma Urine CSF
Lung Colon Adrenal gland
THP-1 Jurkat Granulosa cells
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Proteomics Metabolomics Glycomics
Mass spectrometry – NMR based, 20 dedicated fte, part of diagnostic laboratory (Department of Laboratory Medicine), close interaction with Radboudumc scientists and external partners
Translational Metabolic Laboratory – Laboratory Medicine
Ron Wevers, Jolein Gloerich, Alain van Gool, Leo Kluijtmans, Dirk Lefeber, Hans Wessels, et al
Research Biomarkers Diagnostics
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Mass spectrometry – NMR based, 20 dedicated fte, part of diagnostic laboratory (Department Laboratory Medicine), close interaction with Radboudumc scientists and external partners
Key experts: Proteomics Jolein Gloerich Hans Wessels Alain van Gool Glycomics Monique Scherpenzeel Dirk Lefeber Metabolomics Leo Kluijtmans Ron Wevers
Translational Metabolic Laboratory – Laboratory Medicine
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Research • Projects • Service
External • Projects • Service
Patient care • Health care focus • Biomarkers, diagnostics • Consortia (NL, EU)
Key features: • Expertise centre rather than service facility • Focus to translate Research to Biomarkers to Diagnostics • Application of many years Omics expertise to customer’s specific needs • Ambition to grow with long-term strategic projects, collaborations, staff and impact
Translational Metabolic Laboratory – Laboratory Medicine
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Radboud Proteomics Center
Bottom up proteomics
Top down proteomics
Targeted proteomics
Peptide-based Differential Protein Profiling Relative Quantitation
Intact protein-based Post Translational Modifications
Research Biomarkers Diagnostics
Peptide-based Selected biomarkers Quantitative analysis
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Proteomics techniques
• Peptide-based identification of proteins • Differential protein expression profiling (labelfree/labeled) • Suitable for very complex samples (in combination with fractionation) • Focus on research
Whole proteome analysis
Protein complex isolation and characterization
Bottom up Proteomics
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Applications • Differential protein expression in:
• Health/disease
• Time
• Before/after treatment
• Protein-protein interactions:
• Protein complexes
• Protein correlation profiling
Up regulated Down regulated
Instruments:
Bottom up proteomics
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Proteins Peptides Data Analysis
Ph
ase
1
RP pH2.7 LC-MS/MS
Trypsin
1D LC MS/MS workflow
CONTROLS
CONDITION 1
CONDITION 2
• Body fluids • Circulating vesicles • Tissues • Cells • Organelles • Membranes • Protein complexes • Single proteins
Samples:
Bottom up proteomics
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Example cellular proteome profiling
Sample: HEK293 whole cell proteome (1 µg tryptic digest of urea extract)
1D LC-M/MS proteomics analysis
Retention time
m/z
400
600
800
1000
1200
1400
m/z
10 20 30 40 50 60 Time [min]
Blue: signal intensity in MS Pink dots: precursors selected for MS/MS
Detected peaks in MS spectra 1.584.599
Detected isotope patterns in MS spectra 130.172
Total number of MS/MS spectra 22.743
Av. Absolute Mass Deviation [ppm] 2,8972
Matched MS/MS spectra 5.603
Identified NR peptides 4.537
Identified proteins 1.321
False Discovery Rate 0,98%
Bottom up proteomics
In 1 scan:
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Proteins Peptides RP pH10 UPLC 20 fractions
Ph
ase
1
Ph
ase
2
20 fractions RP pH2.7 LC-MS/MS
Data processing Statistical analysis
400
600
800
1000
1200
m/z
20 30 40 50 Time [min]
Trypsin
CONTROLS
CONDITION 1
CONDITION 2
2D LC (RP x RP) MS/MS workflow
Bottom up proteomics
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719
94
109
41
246
845
1107
2D LC-MS/MS 60min gradients
1D LC-MS/MS 60min gradient
2D LC-MS/MS 20min gradients
963
1851
2765
0
500
1000
1500
2000
2500
3000
1D
LC
-MS/
MS
60
min
2D
LC
-MS/
MS
20
min
2D
LC
-MS/
MS
60
min
1.9x
2.9x
Added value 2D LC-MS/MS
1D RP LC-MS/MS versus 2D RPxRP LC-MS/MS: HEK293 cell line
Bottom up proteomics
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Added value 2D LC-MS/MS
692
1769
0
200
400
600
800
1000
1200
1400
1600
1800
2000
1D LC-MS/MS 2D LC-MS/MSId
en
tifi
ed
pro
tein
s
2.6x
1264
505
187
2D LC-MS/MS 60min gradients
1D LC-MS/MS 60min gradient
1D RP LC-MS/MS versus 2D RPxRP LC-MS/MS: Fat biopt sample
Bottom up proteomics
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Example tissue profiling project Protein expression (positive controls)
GO Protein distributions
Cellular compartments
LFQ scatter plot Biological replicates
y= 0.9834x + 130390 R2=0.9842
Q: downstream effects of transgene? Hippocampus tissue of Transgenic mice 4 Conditions: WT, TG, WT treated, TG treated with drug 5 Biological replicates; 2D LC-MS/MS analysis (20 fractions, 1 hour gradient) Label-Free Quantitation (LFQ – MaxQuant) • LC-MS/MS analyses: 400 •MS spectra: 1.937.394 •MS/MS spectra: 2.323.458 •Detected isotope patterns: 66.602.271 • Isotope patterns sequenced: 1.295.489 • Average absolute mass deviation: 1,38 ppm • 1,3 Terrabyte data
PCA analysis – loading plot
Bottom up proteomics
•Matched MS/MS spectra to peptides: 500.317 • Identified proteins: 3.187 •Quantified proteins: 2.365 (≥2 peptides/protein) •Differential proteins: 276 (p<0.05) • Average CV < 21%* * Combining biological and technical reproducability
Transgene
Downstream
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Proteins SDS-PAGE 9 Gel slices 9 in-gel digests
Ph
ase
1
Ph
ase
2
9 Samples RP pH2.7 LC-MS/MS
Data processing Statistical analysis
400
600
800
1000
1200
m/z
20 30 40 50 Time [min]
Gel enhanced LC-MS/MS workflow
Trypsin
Bottom up proteomics
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Example of cellular proteome profiling project
Q: downstream miRNA effects on proteome? A375 melanoma cell line miRNA treated versus control 3 Biological replicates GeLC-MS/MS analysis (5 slices, 1 hour LC gradients) Label-Free Quantitation (LFQ – MaxQuant) • Identified proteins: 1.932 • Quantified proteins: 1.379 (≥2 peptides/protein) • Differential proteins: 337 (p<0.05) / 151 (p<0.01) • Good reproducibility (average CV < 20%)* • Data analysis: 70% overlap LC-MS/MS and RNA-Seq data * Combination biological and technical reproducability
PCA loading plot
Chromatogram and ion map of a gel fraction
Collaboration with Radboudumc, InteRNA, TNO (DTL hotel project)
Already suspected outlier
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Conclusions
Example of cellular proteome profiling project
Results
Samples
Up regulated
Down regulated
Differential analysis
-10
-5
0
5
10 ∞
∞
178 Differentially expressed proteins
Results
Gene ontology: cellular localization
• 3,824 identified proteins (98.7% cell specific) • 2,550 quantified proteins (≥ 2 peptides/protein) • 178 differential proteins due to treatment:
• 138 proteins upregulated • 40 proteins downregulated
• Good basis for follow-up pharmaco-proteomics
Q: how does proteome cell line x look like? Q: First look at effect treatment on proteome (feasibility) → GeLC-MS/MS approach
Bottom up proteomics
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Cluster: 28S mt-Ribosome
Cluster: 39S mt-Ribosome
Cluster: F1F0 ATP synthase
Cluster: cytochrome b-c1 complex
Cluster: NADH dehydrogenase & TCP1
Cluster: trifunctional enzyme & isocitrate dehydrogenase
Cluster: cytochrome C oxidase & mt-Ribosomal subcomplex
Example of complexome analysis project Bottom up proteomics
Collaboration with NCMD, Bob Lightowlers
Q: What subcomplexes in mitochondrial proteome? HEK293 Mitochondrial fraction 2 BN gel lanes (4-12% AA & 5-15% AA) 24 gel slices per gel lane • Migration profiles for 953 proteins • Unambiguous ID of 24 known complexes • Validation of 8 implied interactors of the mt-Ribosome • 11 novel putative interactors of the mt-Ribosome
Hierarchical clustering
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Fit-for-purpose sample preparation
MARS-14 depletion
GeLC-MS/MS 1D LC-MS/MS 2D LC-MS/MS GeLC-MS/MS 1D LC-MS/MS 2D LC-MS/MS
A B C D E F
Human CSF
Bottom up proteomics
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Q: Changes in exosome proteome related to clinical phenotype?
Samples: - urine exosomes from patients with rejection after renal transplantation
- 4 subject groups (CTRL, REJ, CMV, BK)
Approach: - Gel enhanced 1D LC-MS/MS analysis (9 fractions)
- Per subject group: 2 different pools of multiple patients
- 2 separate experiments (LTQ FT Ultra & MaXis 4G)
Results: - Robust sample preparation is crucial
- In total 521 proteins identified
- Exosome enrichment confirmed by gene ontology classification (Cellular Components)
Collaboration with Department of Urology
Example of urine exosome analysis project Bottom up proteomics
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Anammox batch reactor
PCA analysis – loading plot
2D Hierarchical Clustering
Q: optimal growth conditions? Anammox bacterium 3 Different growth conditions 4 Technical replicates 1D LC-MS/MS analysis (1 hour gradient) Label-Free Quantitation (LFQ – MaxQuant) • Identified proteins: 270 • Differential proteins: 75 • Excellent reproducibility (average CV < 6.5%)
LFQ scatter plot technical replicates
y= 1.0141x + 1250.7 R2=0.9991
Example of biotechnology project Bottom up proteomics
Collaboration with Boran Kartal/Mike Jetten (FNWI RU)
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Q: Effect of two bacterial growth conditions? Desulfobacillus bacterium 2 Different growth conditions; 2 Biological replicates GeLC-MS/MS analysis (9 slices, 1 hour gradient) Label-Free Quantitation (LFQ – MaxQuant) • Identified proteins: 1.228 • Quantified proteins: 950 • Differential proteins: 245 (p<0.05) / 109 (p<0.01) • Excellent reproducibility (average CV < 10%)*
* Biological replicates: technical reproducability likely better
Protein expression example
Example of biotechnology project
LFQ scatter plot Biological replicates
y= 1.0167x - 49244 R2=0.998
PCA loading plot
PC1 (72.9%)
PC
2 (
14
.7%
)
Collaboration with external client
Bottom up proteomics
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Radboud Proteomics Center
Bottom up proteomics
Top down proteomics
Targeted proteomics
Peptide-based Differential Protein Profiling Relative Quantitation
Intact protein-based Post Translational Modifications
Research Biomarkers Diagnostics
Peptide-based Selected biomarkers Quantitative analysis
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Proteomics techniques
• Intact protein analysis • Post-translational modification • Analysis of low to medium
complexity samples
Top down proteomics
LC-MS Ion map of protein complex with MS spectrum of one subunit
Deconvoluted protein spectrum
Instruments:
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Applications
• Characterization of intact
proteins:
• Post-translational
modifications
• Protein processing
• Splice variants
• Protein complex analysis
• Composition
• Complex-specific subunit
variants
• Quality control of biotech
products
Top down proteomics
Quantitative analysis of intact protein isoforms
Collaboration with Floris van Delft (Synnafix)
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Complexes Native Electrophoresis
60 Gel slices 60 in-gel digests
Ph
ase
1
Ph
ase
2
60 Samples RP pH2.7 LC-MS/MS
Data processing Complexome
Profile
400
600
800
1000
1200
m/z
20 30 40 50 Time [min]
Bottom-up Complexome Profiling workflow
Trypsin
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Complexes Native Electrophoresis
Gel slice of interest
Protein extraction, reduction and SPE
Ph
ase
1
Ph
ase
2
Protein sample
LC-MS/MS with fraction collection
Data processing Top-Down profiling
Top-Down Complexome Profiling workflow
Survey View
500
1000
1500
2000
2500
m/z
10 20 30 40 50 60 70 Time [min]
15
24
23
11 128 10 16 17 2618
20919
22211413
12 13 14 15 16 17 18 19 20 Time [min]
0.0
0.5
1.0
1.5
2.0
2.5
7x10
Intens.
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Ph
ase
3
Integrated Complexome Profiling workflow
Protein fractions of interest
Peptides RP pH2.7 LC-MS/MS
Peptide MS2 level Data
nESI-MS/MS Protein MS2
level data
Characterized proteoform
Tryp
sin
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Example of complexome analysis Survey View
500
1000
1500
2000
2500
m/z
10 20 30 40 50 60 70 Time [min]
'1009.716810+
'1121.79549+
'1261.89388+
'1442.02087+ '1682.1905
6+
'2018.42955+
+MS, 56.8-58.7min #3408-3522
0
1
2
3
4
5
4x10
Intens.
1000 1200 1400 1600 1800 2000 2200 m/z
5+
6+
7+
8+
9+
10+
5+
6+ 7+
8+
9+
10+
1.682 m/z Da
Q: Composition of mitochondrial complex 1?
• Y. lipolytica complex 1 as a model for human
• 42 established subunits (7 mtDNA, 35 nDNA)
•Unknown mature subunit forms
•Unknown and dynamic post-translational modifications
• Study: Combine Top-Down and Bottom-Up characterization of all subunits
Collaboration with Ulrich Brandt
Top down proteomics
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Experimental setup
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LC-MS ion map of 40-subunit protein complex Survey View
500
1000
1500
2000
2500
m/z
10 20 30 40 50 60 70 Time [min]
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ESI spectrum of 1 subunit Survey View
500
1000
1500
2000
2500
m/z
10 20 30 40 50 60 70 Time [min]
'1009.716810+
'1121.79549+
'1261.89388+
'1442.02087+ '1682.1905
6+
'2018.42955+
+MS, 56.8-58.7min #3408-3522
0
1
2
3
4
5
4x10
Intens.
1000 1200 1400 1600 1800 2000 2200 m/z
5+
6+
7+
8+
9+
10+
5+
6+ 7+
8+
9+
10+
1.682 m/z Da
![Page 42: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/42.jpg)
Top down / bottom up analysis of subunit protein (13,2 kDa)
Top-Down LC-MS/MS (ETD)
Top-Down NSI-MS/MS (ETD)
Bottom-Up LC-MS/MS (CID & ETD)
Matched peptide sequences in red, amino acids matched as ETD fragment ions are marked yellow (only for Top-Down data)
Hypothesized protein form
• N-terminus processing: Targeting sequence cleavage at S18 • C-terminus processing: None • Additional PTMs: None
Top down proteomics
![Page 43: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/43.jpg)
Overlay deconvoluted experimental and simulated spectra
'10923.3198Mr
'10947.2792Mr
'10961.2630Mr
CI filtered Captive 3ul 05FA_Tray02-E1_01_1071.d: +MS, 11.2-12.1min, Deconvoluted (MaxEnt, 503.10-2187.28, *0.063125, 50000)
CIfilteredCaptive₃ul₀₅FA_Tray₀₂-E₁₀1₁071.d:C₄₈₀H₇₄₃N₁₃₉O₁₅₂S₄, , 11014.3560
CIfilteredCaptive₃ul₀₅FA_Tray₀₂-E₁₀1₁071.d:C₄₇₇H₇₃₄N₁₃₈O₁₅₂S₃, , 10923.3105
0.0
0.2
0.4
0.6
0.8
1.0
6x10
Intens.
0.0
0.2
0.4
0.6
0.8
1.0
1.2
6x10
0.0
0.2
0.4
0.6
0.8
1.0
1.2
6x10
10920 10940 10960 10980 11000 11020 m/z
Measured spectrum
Simulated spectrum - unprocessed form (database entry)
Simulated spectrum - hypothesized form (according to MS/MS results)
Top down proteomics
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Characterization of complex subunits
Q: Composition of mitochondrial complex 1?
•Predicted: 42 subunits (7 mtDNA, 35 nDNA)
•Detected: 240 protein subunit isoforms
(truncations, PTMs)
•Straight but time-consuming path to subunit characterization
Top down proteomics
![Page 45: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/45.jpg)
Intact complexome analysis from tissue biopsies
Pilot study:
• Native tissue biopsies
• Isolate membrane complexes
• Separate and isolate complexes using Blue Native gels
• LC-MS/MS analysis
• Data analysis
Tissue 1 (n=3)
Tissue 2 (n=3)
Subunit
Subunit – tissue 1
Subunit – tissue 2
• Identified protein sequence of subunit • Deduce simulated sequences from database • Determine fit with experimental data
Top down proteomics
![Page 46: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/46.jpg)
Example of diagnostic top-down proteomics
• 12 families with liver disease and dilated cardiomyopathy (5-20 years)
• Initial clinical assessment didn’t yield clear cause of symptoms
• Specific sugar loss of serum transferrin identified via glycoproteomics
ChipCube-LC- Q-tof MS
• Outcome 1: Explanation of disease
• Outcome 2: Dietary intervention as succesful personalized therapy
• Outcome 3: Glycoprofile transferrin developed and applied as diagnostic test
• Genetic defect in glycosylation enzyme (PGM1) identified via exome sequencing
{Tegtmeyer et al, NEJM 370;6: 533 (2014)}
Genomics Glycomics Metabolomics
Top down proteomics
By Monique van Scherpenzeel, Dirk Lefeber
![Page 47: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/47.jpg)
Radboud Proteomics Center
Bottom up proteomics
Top down proteomics
Targeted proteomics
Peptide-based Differential Protein Profiling Relative Quantitation
Intact protein-based Post Translational Modifications
Peptide-based Selected biomarkers Quantitative analysis
Research Biomarkers Diagnostics
![Page 48: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/48.jpg)
Proteomics techniques
• Peptide-based • Sensitive quantitative analysis • Suitable for very complex
samples
Targeted proteomics
Nature Methods: Method of the year 2012
protein expression data
Data Analysis
Protein A isoform 1 Protein A isoform 2 Protein B
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Applications
(Absolute) quantitation of protein biomarkers:
• Biomarker research: Quantitative analysis of specific set of proteins
• Biomarker validation: Validation and prioritization of selected biomarkers
• Diagnostics: Analysis of qualified biomarkers
Targeted proteomics
Research Diagnostics
Instruments:
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Biomarker innovation gap
• Imbalance between biomarker discovery, validation and application
• Many more biomarkers discovered than available as diagnostic test
50
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Selection of biomarkers
Single Reaction Monitoring workflow P
has
e 1
Selection of optimal peptides
• Unique • Best detectable in LC-MS
Optimize detection by selecting optimal transitions
Ph
ase
2
Proteins Peptides Data Analysis RP pH2.7 LC-MS/MS
Trypsin
Isotope labeled
standards
Isotope labeled
standards
Targeted proteomics
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LCM-proteomics workflow
Laser Captue Microdissection Sa
mp
le p
rep
arat
ion
Proteins
Trypsin
Peptides 9 µm tissue
sections
LC-M
S/M
S
Data Analysis Targeted SRM Data Analysis
CONTROLS
CONDITION 1
CONDITION 2
1D LC-MS/MS
Biomarker Discovery Biomarker Validation
Targeted proteomics
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• Proteomics • Bottom-up (shot-gun) proteomics • Targeted proteomics • Top-down proteomics
• Glycomics
• Glycan profiling • (Targeted) Glycoproteomics
• Metabolomics
• Untargeted metabolomics • Targeted metabolite profiling
Translational Metabolic Laboratory – Laboratory Medicine
Research Biomarkers Diagnostics
Key experts: Jolein Gloerich Hans Wessels Alain van Gool Monique Scherpenzeel Dirk Lefeber Leo Kluijtmans Ron Wevers
![Page 54: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/54.jpg)
Source: Allison Doerr, Nature Methods 9,36 (2012)
Glycomics
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Glycosylation markers in human medicin
• Biomarker for disease and therapy monitoring: rheumatoid arthritis,
oncology, hepatitis • MUC2 glycosylation in colon carinoma • Human blood groups (A, B, O, AB)
• CDTect (Carbohydrate-Deficient transferrin) • Infectious diseases • IgA nephropathy
1% of genes directly involved in glycosylation About 50% of proteins is glycosylated
IgA
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Glycosylation types
• N-glycosylation
• Asparagin linked • 8 - 20 saccharides
• O-glycosylation
• Serine/Threonine linked • <10 sacchariden
• Glycosaminoglycans
• 100-200 disaccharide units • Agrin, Perlecan, Syndecan, Glypican
• Glycolipids
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Diagnostics Research
Urinary glycan profiling
Serum glycan profiling
O-glycan profiling
PNGaseF chip
Chemical biology
Glycopeptide profiling
glycolipid profiling
Whole protein glycoprofiling
Nucleotide-sugars
Glycomics approaches
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Glycomics application areas
• Mechanisms of glycosylation disorders
Linking genes to glycomics profiles
Understanding neuromuscular pathophysiology
• Glycomics Technology Platform Services
Functional foods
Glycan tracers
Biomarkers
![Page 59: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/59.jpg)
Glycomics
Intact glycoprotein
Free glycans
Glycopeptides 500
750
1000
1250
1500
1750
m/z
10 15 20 25 30 35 40 Time [min]
PGM1 profile
CID fragmentation spectrum
![Page 60: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/60.jpg)
Example: Intact glycoprotein biomarker
• 12 families with liver disease and dilated cardiomyopathy (5-20 years)
• Initial clinical assessment didn’t yield clear cause of symptoms
• Specific sugar loss of serum transferrin identified via glycoproteomics
ChipCube-LC- Q-tof MS
• Outcome 1: Explanation of disease
• Outcome 2: Dietary intervention as succesful personalized therapy
• Outcome 3: Glycoprofile transferrin developed and applied as diagnostic test
• Genetic defect in glycosylation enzyme (PGM1) identified via exome sequencing
{Tegtmeyer et al, NEJM 370;6: 533 (2014)}
Genomics Glycomics Metabolomics
60
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Example: Glycopeptide profiling
• Optimized procedure using simple sample prep of plasma • Detection of ~12.000 unique deconvoluted monoisotopic masses per
single analysis (> 50% are glycopeptides)
500
1000
1500
2000
m/z
5 10 15 20 25 30 35 40 Time [min]
Proof of principle study:
Monique van Scherpenzeel, Dirk Lefeber, Hans Wessels, Alain van Gool Translational Metabolic Laboratory, Radboudumc, unpublished data
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Example: Glycan analysis by nanoChip-QTOF MS
• High-resolution glycoprofiling
• Microfluidic chip system results in simplified operating conditions, increased reproducibility and robustness
• CHIP formats: C18, Carbograph, C8, HILIC, phosphopeptides, PNGaseF
![Page 63: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/63.jpg)
Bio-informatics : • Coupling with public glyco-databases • Annotation of glycan linkages
Glycan profiling in serum
B4GalT1
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• Proteomics • Bottom-up (shot-gun) proteomics • Targeted proteomics • Top-down proteomics
• Glycomics
• Glycan profiling • (Targeted) Glycoproteomics
• Metabolomics
• Untargeted metabolomics • Targeted metabolite profiling
Translational Metabolic Laboratory – Laboratory Medicine
Research Biomarkers Diagnostics
Key experts: Jolein Gloerich Hans Wessels Alain van Gool Monique Scherpenzeel Dirk Lefeber Leo Kluijtmans Ron Wevers
![Page 65: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/65.jpg)
Metabolomics approaches
Diagnostics • Organic acids • Amino acids • Purines&Pyrimidines • Monosaccharides/Polyols • Carnitine(-esters) • Sterols
Research • Assay development for specific
metabolites or metabolite classes • Untargeted metabolite profiling • Metabolite biomarker identification
Equipment • GC • 2 GC-MS • 3 LC-MS/MS • 2 amino acid analysers • HPLC
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Example: targeted diagnostics in metabolic disease
Amino acids Amino acid analyser
Carnitine-ester profile LC-MS/MS
Purines & pyrimidines - HPLC & LC-MS/MS
Organic acids GC-MS
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DIAGNOSIS OF INBORN ERROR OF METABOLISM
Example: untargeted metabolomics to diagnose individual patients
Human plasma
20 controls vs 1 patient
Agilent QTOF MS-data
- Reverse phase liquid chromatography - Positive mode - Features
•Accurate mass (165.07898) • Retention time • Intensity
XCMS Alignment Peak comparison > 10000 Features
Chemometric pipeline • T-test • PCA • P95
Metabolite identification Online database HMDB
phenylalanine
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Integrated databases
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A blind study
Plasma sample choice : Dr. C.D.G Huigen
Analytical chemistry : E. van der Heeft
Chemometrics : Dr. U.F.H. Engelke
Diagnosis : Prof. dr. R.A. Wevers;
Dr. L.A.J. Kluijtmans
Test 10 samples from 10 patients with 5 different
Inborn Error of Metabolism’s
21 controls
![Page 70: Overview Radboudumc Center for Proteomics, Glycomics and Metabolomics april 2015](https://reader033.vdocuments.mx/reader033/viewer/2022042716/55a6f43c1a28abba1f8b46bc/html5/thumbnails/70.jpg)
The blind study
MSUD (2) → leucine, isoleucine, valine, 3-methyl-2-oxovaleric acid
Aminoacylase I deficiency (2) → N-acetylglutamine, N-acetylglutamic acid, N-acetylalanine, N-acetylserine, N-acetylasparagine, N-acetylglycine
Prolinemia type II (2) → proline, 1-pyrroline-5-carboxylic acid
Hyperlysinemia (2) → pipecolic acid, lysine, homoarginine, homocitrulline
3-Hydroxy-3-methylglutaryl-CoA lyase deficiency (2) → 3-methylglutaryl-carnitine, 3-methylglutaconic acid, 3-hydroxy-2-methylbutanoic acid, 3-hydroxy-3-methylglutaric acid
Diagnostic metabolites found in blood plasma
• Correct diagnosis in all 10 patients
• Five different IEM’s identified by
differential metabolites
• The approach works!!!
• Validated method diagnostic SOP
• Planned for execution in line with genetics
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2012
Patient Targeted
Metabolic
screen
Targeted
gene
analysis
Diagnosis
+ follow-up
2013 / 2014
Patient
Whole
exome
sequencing Targeted
confirmatory
metabolite +
enzyme
testing
Diagnosis
+ follow-up
Targeted assays vs holistic approach
Next
generation
metabolic
screening
Times are changing… (functional) genome analysis
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Human samples
Plasma, CSF (urine) Controls vs. patient
QTOF Mass Spectrometry
- Reverse phase liquid chromatography - Positive and negative mode - Features
XCMS Alignment Peak comparison > 10,000 Features
Personalized metabolic diagnostics
Xanthine Uric acid
72
Full metabolite profile: Highly suspected of xanthinuria
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• Proteomics • Bottom-up (shot-gun) proteomics • Targeted proteomics • Top-down proteomics
• Glycomics
• Glycan profiling • (Targeted) Glycoproteomics
• Metabolomics
• Untargeted metabolomics • Targeted metabolite profiling
Translational Metabolic Laboratory – Laboratory Medicine
Research Biomarkers Diagnostics
Key experts: Jolein Gloerich Hans Wessels Alain van Gool Monique Scherpenzeel Dirk Lefeber Leo Kluijtmans Ron Wevers
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A problem in biomarker land
Imbalance between biomarker discovery and application.
• Gap 1: Strong focus on discovery of new biomarkers, few biomarkers progress beyond initial publication to multi-center clinical validation.
• Gap 2: Insufficient demonstrated added value of new clinical biomarker and limited development of a commercially viable diagnostic biomarker test.
Discovery Clinical validation/confirmation
Diagnostic test
Number of biomarkers
Gap 1
Gap 2
74
The innovation gap in biomarker research & development
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Some numbers
Data obtained from Thomson Reuters Integrity Biomarker Module
Eg Biomarkers in time: Prostate cancer May 2011: 2,231 biomarkers Nov 2012: 6,562 biomarkers Oct 2013: 8,358 biomarkers 25 Sep 2014: 9,975 biomarkers with 31,403 biomarker uses
EU: CE marking
USA: LDT, 510(k), PMA
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Shared biomarker research through open innovation
We need to set up a open innovation network to share biomarker knowledge and jointly develop and validate biomarkers (at level of NL and EU):
1. Assay development of (diagnostic) biomarkers
2. Clinical biomarker quantification/validation/confirmation
Shared knowledge,
technologies and objectives
Funding: NL – STW; EU - Horizon2020, IMI; Fast track pharma funds
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Good example of multi-center biomarker validation
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Biomarker Development Center (Netherlands)
STW perspectief grant
Biomarker Development Center
Public-private partnership 4 years
Project grant 4.3M Eur of which 2.2M government,
and 2.1M industry (0.9M cash/1.2M kind)
Close interactions with:
- Clinicians (biomarker application)
- Industry
- Patient stakeholder associations
Open Innovation Network !
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healthy disease disease + treatment
Challenge: how to identify subpopulations in Personalized Healthcare?
healthy disease disease + treatment
• Biomarkers in populations often have a wide range • Within this range, subpopulations can behave quite differently • Chemometric methods dealing with multiple biomarker data points are needed
to reveal such individual differences and enable personalized medicine
(Source: Jasper Engel, Lionel Blanchet, Udo Engelke, Ron Wevers and Lutgarde Buydens)
80
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Approach Multiple
biomarker datapoints
Chemometrics Kernel transformation
Biosamples
Apply methods to identify subpopulations for Personalized Medicine
Urine NMR
81
(Source: Jasper Engel, Lionel Blanchet, Udo Engelke, Ron Wevers and Lutgarde Buydens)
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Contact information
• Proteomics
• Glycomics
• Metabolomics
• Biomarkers
Visiting address: Radboud umc, route 774/830 https://www.radboudumc.nl/Research/ProteomicsMetabolomicsGlycomics/
http://laboratorymedicine.nl/104_theme_104_Translational-Metabolic-Laboratory.html
[email protected] [email protected] Alain.van [email protected] [email protected] [email protected] [email protected] [email protected] Alain.van [email protected] [email protected]