Sample Preparation Automation and QQQ …...3.0 amol on-column 5.0 amol on-column 7.5 amol on-column...
Transcript of Sample Preparation Automation and QQQ …...3.0 amol on-column 5.0 amol on-column 7.5 amol on-column...
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Sample Preparation Automation and QQQ Workflows for
Peptide Quantitation in DMPK
Alex Zhu & Yanan Yang
LCMS Applications Scientist
Agilent Technologies
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Why is Agilent Workflow a Good Choice for DMPK?
AssayMAP
Automated Sample Prep
Quantitation with confirmation
Simple MRM method development
Great Robustness
Excellent Reproducibility
Ultra High Sensitivity
wide dynamic range
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Sample Prep. Method Dev. Data
Acq.
Data
Ana.
Agilent Workflow for DMPK
Skyline
AssayMAP Bravo MH Quant 6495 QQQ
tMRM Skyline
6495 QQQ
App Library
All Ions MSMS
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AssayMAP Technology Components
Microchromatography
Cartridges Quantitative binding & elution
Protein purification
• PA-W (protein A)
• PG-W (protein G)
• SA-W (streptavidin)
Reversed-phase cleanup:
• C18 (peptide)
• RP-S (peptide)
• RP-W (denatured mAbs)
Peptide Fractionation:
• SCX
• RP-S
• C18
Phosphopeptide enrichment:
• TiO2
• Fe(III)-NTA
Positive Displacement Pipetting Syringes interface directly with cartridges and
enable precise, controlled liquid flow through
cartridges with no air bubbles to disrupt binding
Simple User Interface Uses customer language - not
automation language
• Affinity (protein) Purification
• In-Solution Digestion
• Peptide Cleanup (desalting)
• Protein Cleanup (desalting)
• Phosphopeptide Enrichment
• IMAC Cartridge Customization
• Fractionation
• Sample Normalization
• Liquid handling utilities
Target Customer
Automated workflows designed for analytical chemists
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Workflow Library
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Workflows
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Purification Reproducibility and Recovery Using
PG-W Cartridges
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1
2 3
4
5 6
Consistent and Robust
Across 96
sample replicates
EIC overlays of mAb peptides from a single row of samples (n = 12)
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• Affinity
purification
• Denaturing
• Reduction
• Alkylation
• Digestion
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AssayMAP Power Users
Daniel Spellman (Merck, West Point, USA)
Field: large molecule pharmacokinetics
AssayMAP Application: enrichment, digestion, cleanup
Dan has made AssayMAP a critical part of a workflow used at Merck. AssayMAP
provides significant reductions in both consumable cost and time to results. No
more messy mag beads!
Jacob Jaffe, The Broad Institute in Cambridge and MIT, USA
Field: High-Throughput Proteomics
AssayMap Application: mAb & phosphopeptide enrichment, digestion, cleanup
"Using the combination of extremely consistent, parallelized digestion with
automated reverse-phase cleanup via AssayMAP, at a scale appropriate for
ultrasensitive proteomics applications, has enabled us to contemplate collaborative
studies of previously unheard-of scales and throughput.”
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Kevin Bateman (Merck-WP, European Bioanalysis Forum, Barcelona Nov 2014
Magnetic Bead AssayMAP
Comparison Standard vs. High Throughput
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6495 QQQ LC/MS - Premium Performance
Improved sensitivity (IDL / MDL) – Average 3x in S/N for peptides comparing to 6490
Improved precision and excellent accuracy at the lowest levels
Proven 6 orders of linear dynamic range
Proven robustness in complex matrix –biological matrix (plasma)
Improved mass range (2250), fast scan speed and MRM acquisition rate
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Enhancing Sensitivity for Higher Flow LC Using
More Efficient Ionization of Peptides
2 x10
0.2
0.4
0.6
0.8
1.0
Acquisition Time (min) 3 3.5 4 4.5 5 5.5 6 6.5 7
1 2 3 4 5 6 7 AJS normalized response
ESI relative response
MS Inlet
Heated Sheath Gas
Thermal Gradient Focusing Region
Heat Sink with Active Cooling
Agilent JetStream interface:
• Thermal gradient focusing electrospray
• Usable with flow rates from 10 µL/min and up
• Yields 3-5x increase in sensitivity for peptides
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Agilent Jet Stream
Off On
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Enhancing Sensitivity by Increasing Ion Sampling
and Transmitting
Samples
more ions
Removes
neutrals
Gives
higher
ion yield
High
Pressure
Stage 1
Low
Pressure
Stage 2
Existing
RF Ion
Guide
6 Bore
Capillary
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6495 QQQ Technologies
Continued Development
1 2
3
• New Detector with High Energy Conversion Dynode
• Improved ion detection with low noise 3
• New Tapered Hexapole Collision Cell
• Effective ion collection and transmission 2
Proven iFunnel Technology • Agilent Jet Stream
• Hexabore Capillary
• Dual Ion Funnel
• Increased ion generation
• Enhanced ion sampling
• New Enhanced Q1 Ion Optics
• Improved ion transmission 1
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Collision Energy Optimization Using Skyline SW
CE
Replicate
0
10
20
30
40
50
60
P e
a k
A r e
a (
1 0
3
)
CE
Replicate
0
10
20
30
40
50
60
P e
a k
A r e
a (
1 0
3
)
Opt CE
Skyline SW will export MRM list or acquisition method to run on Agilent QQQ
with optimal CE for each transition
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Agilent QQQ and Skyline Software
Automation Tool for Automatic CE optimization
Automation tool automatically
creates QQQ methods and
acquires data for CE
optimization, reloads and
analyzes the results, exports
the final optimized QQQ
method (MRM, dMRM, tMRM)
and use it to runs any real
samples queued up in the
worklist
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Agilent QQQ and Skyline Software
Automation Tool for Automatic CE optimization
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Challenges
No prediction for representative peptides/preferred charge
state.
Numerous runs for collision energy optimization based on the
number of proteins and peptides.
Questionable prediction for modified peptides.
Thursday, September 03, 2015
Mayo CMSL Mass Spec Overview
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y3+
y5+ y12++
y14++
y8+ y9+
y10+ y11+ y7+
CE=0
CE=25 V
mAb Tryptic Digest
p++
P 3+
P 2+
Simplified MRM Method Development: Agilent All Ions MS/MS on a QTOF + Skyline SW
Thursday, September 03, 2015
Mayo CMSL Mass Spec Overview
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Method Development for Multiple Proteins
Method development for multiple proteins can be done from the same All Ions result, simultaneously or at a later time.
Import a different protein sequence and load the same All Ions data. Same procedure followed.
Thursday, September 03, 2015
Mayo CMSL Mass Spec Overview
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Skyline Prediction Workflow vs. All Ions-Skyline Workflow
mAb Tryptic Digest Skyline Prediction Workflow All Ions – Skyline Workflow
Number of peptides for CE
optimization
40 3
(Selected by All Ions run)
Injections required for CE
optimization
40
(One inj. for one peptide)
3
Total time required for MRM method
development
40×10 = 400 min (3+1)×10=40 min
(1 is for All Ions run)
Save up to 90% of time and 90% of samples needed for method development
Thursday, September 03, 2015
Mayo CMSL Mass Spec Overview
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Triggered MRM
Threshold
Peptide 3 triggers
Peptide 3 triggers secondary transitions,
collects ‘n’ cycles & goes back to primary cycle
Primary cycle (below threshold)
Triggered cycle (above threshold)
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Quantitation with Confidence
Qualifier to Quantifier Ratio Reference vs. experiment
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Ultra High Sensitivity: Low Attomole LLOD 2.1 mm ID column w AJS and Hexabore = Cap LC Detection
blank
3.0 amol
on-column
5.0 amol
on-column
7.5 amol
on-column
Instrumentation: 1290 UHPLC + Agilent JetStream + 6495 QQQ
Sample: synthetic peptide standard (LVNEVTEFAK) spiked into enolase tryptic digest
Injection volume: 1 µL
LLOD
LLOQ
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Excellent Precision at LLOQ,
2.1 mm ID column w AJS + Hexabore = Cap LC
DDetection
Amount measured Replicates %RSD t (99%) IDL
5.0 amol (LLOQ) n = 10 injections 14.0 2.821 2.0 amol
MDL = t x (%RSD/100) x Amount = 2.821 x (14.0/100) x 5.0 amol = 2.0 amol
Inj # Peak
Area
1 30.5
2 28.7
3 30.4
4 33.91
5 35.1
6 31.5
7 34.5
8 20.7
9 26.7
10 26.6
%RSD 14.0
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Six Orders of Dynamic Range
Zoom-in 5 – 500 amol
LVNEVTEFAK
5 amol – 5 pmol on-column
6 orders of linear dynamic range
R2 = 0.998
LVNEVTEFAK
Calibration Standards (amount on-column; 1 µL injected)
5.0
amol
7.5
amol
15
amol
30
amol
300
amol
3
fmol
30
fmol
300
fmol
3
pmol
5
pmol
%Accuracy 109.8 108.7 105.0 87.1 85.2 81.4 86.4 87.4 105.6 97.5
Reproducibility
(%RSD, n=10) 14.0 16.0 9.4 9.0 1.6 1.2 0.6 0.7 2.1 1.0
RT (%RSD, n=100) 0.12
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Peptide X - 8 Levels, 8 Levels Used, 47 Points, 47 Points Used, 0 QCs
Concentration (ng/ml)
-5 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105
R e
s p
o n
s e
s
4 x10
-0.1
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1
1.1
1.2
1.3
1.4
1.5
y = 141.655763 * x + 1.897223
R^2 = 0.99805733 Type:Linear, Origin:Ignore, Weight:1/x
mAb Peptide in Serum Matrix
Peptide External Calibration Concentration (1 µl injection)
10 amol 25 amol 50 amol 100 amol 250 amol 500 amol 1 fmol 5 fmol
Accuracy (%, n=6) 90.70 106.43 92.83 105.93 96.68 103.63 103.07 99.15
Cal. Conc. %RSD (n=6) 14.38 10.22 16.89 4.36 4.92 3.93 3.09 2.73
Retention Time %RSD (n=48) 0.17%
Range: 10 amol to 5 fmol
R2>0.998
Type: Linear, Origin: Ignore, Weight:1/x
Zoom in: 10-250 amol
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MassHunter Quant: Compound-at-a-glance
Blank
10 amol
25 amol
50 amol
100 amol
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Increased Mass Range Useful for Peptides
QQQ MRM spectrum for glycopeptide: EEQYN[+1606.6]STYR (G1F)
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Proven System Robustness in Complex Matrix:
Protein Quantitation in Plasma Hexabore with six 0.6 mm ID Capillaries is more Robust
and has better peak shape Vs a single large Diameter orifice
• Selected peptides from 42 peptides in the QC sample – normalized to Day 1 response
• Peptide QC samples analyzed daily after every ~25 plasma digest injections
• No significant signal degradation observed after 853 injections of 40 µg plasma
digest per injection and 3.5 weeks of continuous operation
• Response %RSD: 6 - 15
0.00%
20.00%
40.00%
60.00%
80.00%
100.00%
120.00%
140.00%
01/06/14 01/11/14 01/16/14 01/21/14 01/26/14 01/31/14 02/05/14
Apolipoprotein E
L-selectin
Plasminogen
Albumin_serum
Kininogen
Transthyretin
Hemopexin
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Summary
• Automated sample prep: Automated sample cleanup, enrichment
and protein digestion using AssayMap platform
• Sensitive: low attomole LLOQ for peptides with standard flow
• Wide dynamic range: six orders
• Reproducible: small CV at low levels
• Robust: less down time and less need for maintenance
• Simple MRM method development: automated optimization of CE;
All Ions MSMS-Skyline workflow
• Quant with confidence: triggered MRM
• Easy to use quantitative analysis software
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