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CQA Assessment by Peptide Mapping Using LC/MS with an AdvanceBio Peptide Plus Column
Anne Blackwell, Ph.D.
BioColumns Product Support Scientist
June 7, 2017
ASMS
1
For Research Use Only. Not for use in diagnostic procedures.
Analytical groups are tasked with method development, sample analysis, and method transfer
Centrifuge
Biomarker ID
& validation
DNA
Vector
HT Clone
Screening &
Selection
mAb Generation Platform
e.g. transgenic mice Cell Culture Scale-up & Production
Human
gene
Establishment of genetically
engineered cells (e.g. CHO) that
produce desired product
Analytical Groups Develop analytical methods;
analyze samples from other
functions, methods transfer
QA/QC
Samples Samples Samples Samples
Samples Samples
Methods
Market Manufacturing Pre-clinical Clinical Chromatography
Column #1
Chromatography
Column #2
Chromatography
Column #3
2
For Research Use Only. Not for use in diagnostic procedures.
Pyro-
Glutamate
Deamidation
/Oxidation
Fragmentation
(Hinge)
Glycosylation
(G0, G1, G2)
Truncation
(Lys 0, 1, 2)
Disulfide
Shuffling
Aggregation
HILIC
IEC
IEC
IEC
RP
SEC
RP
LC/MS Intact mass
Fragment mass
Identification
PTM ID & locations
Glycan ID
Critical Quality Attributes & Testing Methods
Not just used for monoclonal antibodies – same techniques
are used for any potentially therapeutic protein
3
For Research Use Only. Not for use in diagnostic procedures.
Peptide Mapping Workflow Solutions to Accelerate Biomolecule Characterization
4
Delivery of Results
Reporting
Sequence Matching
Determine Post Translational
Modifications
Data Acquisition
Sample Preparation
Chromatographic Separation
Complete Agilent Workflow Solution
B(6
7-7
3)
B ( 6 0 - 6 6 )
A(1
03
-10
6)
B(3
30
-33
7)
B(2
78
-29
1)
Peptide mapping chromatogram Peptide ID by MS/MS
For Research Use Only. Not for use in diagnostic procedures.
Sample Preparation
Denaturation, Reduction, &
Alkylation
Digestion
Enrichment & Cleanup
Sample Preparation for Peptide Mapping Depletion of matrix proteins,
enrichment of target protein,
dialysis or desalting
Reduce disulfide bonds, and
block to prevent re-formation
Trypsin is the most common
digestion enzyme, but others may
be called for depending on the
protein and experiment.
Sample concentration, enrichment
for specific PTMs, or desalting
A time consuming, labor-intensive process
to do manually, with multiple steps that can
be optimized.
5
For Research Use Only. Not for use in diagnostic procedures.
AssayMAP Bravo – Sample Prep Automation
6
Peptide mapping
Detect
For Research Use Only. Not for use in diagnostic procedures.
AssayMAP Sample Prep Portfolio
Fractionation
Antibody
Purification
Immunoaffinity
Purification
Phosphopeptide
Enrichment
N-glycan
Sample Prep
Protein
Digestion
Peptide Clean
Up
Protein Clean
Up
7
For Research Use Only. Not for use in diagnostic procedures.
General Considerations for Peptide Mapping Column Selection
Instrument capabilities and requirements - UV vs MS detection or both
- Pressure capabilities
Mobile phase requirements - High pH required for sample
- TFA vs Formic acid
Sample - Hydrophilic vs hydrophobic peptides
- Larger polypeptides present
Column dimensions - Generally prefer longer columns, especially for more complicated maps
- 50, 150, and 250 mm lengths available
- Use 2.1 mm i.d. for MS-sensitivity
- 3.0 and 4.6 mm i.d. also available
- Smaller pore sizes ideal, usually 100-150 Å
8
For Research Use Only. Not for use in diagnostic procedures.
Detectors for Peptide Mapping
UV
• Often used in routine process measurements,
QA/QC labs
• No peptide mass or structural information; relies on
reproducibility of RT, peak area, and peak area
ratios
• Traditionally uses TFA modifier
MS
• Often used in discovery/early development
stage, R&D labs
• MW and structural information (MS/MS) to
assist with co-elution challenges, verify
sequence coverage, and to ID unknown peaks
when they appear
• Generally prefer formic acid modifier to avoid
ion suppression from TFA
9
For Research Use Only. Not for use in diagnostic procedures.
Mobile Phases for Peptide Mapping
Ion pairing agents used for RP LC
• Increase retention of small, poorly retained peptides
• Block exposed silanol sites on silica-based columns
• Acid helps solubilize and ionize peptide and protein samples
TFA works well on “traditional” silica-
based columns, but formic acid does not
• Formic acid produces broad, asymmetric peaks
• Poor resolution and poor peak capacity
Need column solution for formic acid
modifier
• AdvanceBio Peptide Plus
• Charged surface chemistry solves the problems associated with formic acid
10
For Research Use Only. Not for use in diagnostic procedures.
Agilent Bio-LC Column Portfolio Agilent Bio-LC Columns
Affinity
Bio-Monolith Protein A
Bio-Monolith Protein G
Multiple Affinity Removal System
Reversed Phase
AdvanceBio Peptide Plus
AdvanceBio Peptide Mapping
AdvanceBio RP mAb
AdvanceBio
Oligonucleotides
AdvanceBio Desalting-RP
PLRP-S
ZORBAX RRHD 300Å, 1.8 µm
AdvanceBio Amino Acid Analysis
ZORBAX Amino Acid Analysis
ZORBAX 300SB
Poroshell 300
HILIC
AdvanceBio Glycan Mapping
ZORBAX RRHD 300-HILIC
Size Exclusion
AdvanceBio SEC
Bio SEC-3
Bio SEC-5
ProSEC 300S
ZORBAX GF-250
ZORBAX GF-450
Ion Exchange
Bio mAb
Bio IEX
(SAX, SCX, WAX, WCX)
PL SAX
PL SCX
Bio-Monolith
(QA, DEAE, SO3)
11
For Research Use Only. Not for use in diagnostic procedures.
Agilent Bio-LC Column Portfolio
Agilent Bio-LC Reverse Phase Columns for Protein Analysis
Intact Proteins (& Fragments)
PLRP-S, 5 µm, 1000 Å
AdvanceBio RP mAb
ZORBAX RRHD 1.8 µm, 300 Å
ZORBAX 300SB
Poroshell 300
AdvanceBio Desalting-RP
Peptides
AdvanceBio Peptide Plus
AdvanceBio Peptide Mapping
ZORBAX Eclipse Plus C18
ZORBAX 300SB*
Amino Acids
AdvanceBio Amino Acid Analysis
ZORBAX Amino Acid Analysis
12
*unusually large pore size for peptide mapping,
but some people really like it nonetheless For Research Use Only. Not for use in diagnostic procedures.
AdvanceBio Peptide Plus
Poroshell particle UHPLC performance at lower pressure
Unique charge hybrid/C18 bonded phase Improved peak shape and peak capacity for peptide
analysis with formic acid and MS detection
To provide AdvanceBio Peptide Plus that gives
benefits in accuracy and reproducibility of results
for characterization of mAb identity, PTMs
13
For Research Use Only. Not for use in diagnostic procedures.
Columns Individually Tested for Efficiency
14
AdvanceBio Peptide Plus Column
For Research Use Only. Not for use in diagnostic procedures.
Column Lots QA Tested Specifically for Peptide Separations
15
Peptides Standard
(p/n G2455-85001) AdvanceBio Peptide Plus Column For Research Use Only. Not for use in diagnostic procedures.
LC/MS Instrumentation
16
• 1290 Infinity II LC system
• 6545XT AdvanceBio LC/Q-TOF
• BioConfirm B.08 for intact protein
and peptide mapping data analysis
For Research Use Only. Not for use in diagnostic procedures.
6545XT Features for Peptide Mapping
• Sensitive peptide detection featuring Agilent Jet Stream
• Quick-start peptide mapping method
• Access low intensity peptides/PTMs with the new
IterativeMS/MS mode
• Sub-ppm mass accuracy with 50k resolution from
improved beam optics
• Peptide fragmentation performance verification at
install
• Ease of maintenance with vent-free capillary removal
For Research Use Only. Not for use in diagnostic procedures.
For Research Use Only. Not for use in diagnostic procedures.
Method Conditions
18
Parameter 1290 Infinity II LC
Column AdvanceBio Peptide Plus 2.1 × 150mm, 2.7µm, 120Å
Mobile phase A: 0.1%FA
B: 0.1% FA in ACN
Gradient
Time (min) %B
0 3
1 3
31 40
33 95
34 95
34.1 3
Post time 10 min
Inj vol 1 µL
Sample thermostat 5 °C
Post time 5 min
Column temp 55 °C
Flow rate 0.5 mL/min
Parameter 6545XT AdvanceBio LC/Q-TOF
Ion mode Positive ion mode, dual AJS ESI (profile)
Drying gas temp 325 °C
Drying gas flow 13 L/min
Sheath gas temp 275 °C
Sheath gas flow 12 L/min
Nebulizer 35 psi
Capillary voltage 4000 V
Fragmentor voltage 175 V
Skimmer voltage 65 V
Oct RF Vpp 750 V
Acquisition parameters Data were acquired at 2 GHz Extended Dynamic
Range
MS mass range 100–1700 m/z
MS/MS mass range 50 – 1700
MS scan rate (spectra/second): 8
MS/MS scan rate (spectra/second): 3
Ramped collision energy
Charge state Slope Offset
2 3.1 1
3 and > 3 3.6 –4.8
Data analysis BioConfirm software B.08.08
All results shown are with formic
acid mobile phase
For Research Use Only. Not for use in diagnostic procedures.
Effect of Flow Rate on Peak Capacity
For Research Use Only. Not for use in diagnostic procedures.
19
TIC
• Increasing the flow rate from 0.1 mL/min to
0.5 mL/min leads to an increase of twice the
peak capacity
8x10
0
0.5
1
1.5
8x10
0
0.5
1
8x10
0
0.5
1
8x10
0
0.5
1
8x10
0
0.5
1
1.5
8x10
0
0.5
1
1.5
Counts vs. Acquisition Time (min)1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63
0.1 ml/min
0.2 ml/min
0.3 ml/min
0.4 ml/min
0.5 ml/min
0.6 ml/min
AdvanceBio Peptide Plus Column
Effect of Gradient Length on Peak Capacity
For Research Use Only. Not for use in diagnostic procedures.
20
• Increasing the gradient time from 0 min to 60 min
leads to an increase 2.5 times peak capacity,
• After 30min, no significant increase in peak capacity
TIC
8x10
0
0.5
1
1.5
8x10
0
0.5
1
8x10
0
0.4
0.8
1.2
8x10
0
0.4
0.8
1.2
8x10
0
0.4
0.8
1.2
8x10
0
0.4
0.8
1.2
Counts vs. Acquisition Time (min)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63
10 min
20 min
30 min
40 min
50 min
60 min
AdvanceBio Peptide Plus Column
Effect of Temperature on Peak Capacity
For Research Use Only. Not for use in diagnostic procedures.
21
LC/MS Chromatogram
• Higher temperature produces narrower peaks, improving resolution
• Change in temperature changes selectivity
• ~20% more peaks resolved by increasing the column temperature to 550C 6x10
0
1
2
6x10
0
1
2
3
Co unts vs. Acquisition Time (min)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
45oC
55oC
Pc = 504
Pc = 600
AdvanceBio Peptide Plus Column
Good Peak Shape & Retention Time Stability with High Mass Load
22
Sample: 3-peptide
mixture in 0.1%FA
• Bradykinin
• Angiotensin II
• Venin substrate
All 2.1 x 50 mm columns
0.6 ug
6 ug
0.6 ug
6 ug
0.6 ug
6 ug
AdvanceBio Peptide Plus
Cortecs Kinetc
0.6 ug
6 ug
AdvanceBio Peptide Mapping
Key for transferring
methods between
LC/MS and LC/UV
For Research Use Only. Not for use in diagnostic procedures.
AdvanceBio Peptide Plus Competitor 1
Competitor 2 Competitor 3
Highly Reproducible Separations
23
n = 10 %RSD
Peak no. RT FWHM Area Height
1 0.20 1.13 0.31 1.36
2 0.06 1.57 5.76 2.54
3 0.06 1.55 4.27 1.39
4 0.06 1.02 4.60 1.23
5 0.07 0.91 3.41 1.53
6 0.05 0.86 2.69 0.74
7 0.06 3.22 5.79 3.33
8 0.04 0.99 3.81 1.12
9 0.02 0.92 2.66 1.31
10 0.02 0.95 4.22 1.80
8x10
0
1
2
3
4
5
Acquisition Time (min)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
Cou
nts
Hydrophilic Hydrophobic
• Consistent chromatography
• RSD values demonstrate the robustness of the method
and precision of the LC system
• Especially crucial for LC/UV peptide mapping
1
2
3
4 5
6
7
8
9
10
AdvanceBio Peptide Plus Column
For Research Use Only. Not for use in diagnostic procedures.
Lifetime Testing
24
Plates dropped < 10%
Rt dropped < 10%
Retention time %
Plates count %
• The column has subjected to 1000
injections and lost no more than 10%
of the initial plate and retention value
at the end of the test
• Good chemical stability under formic
acid conditions
Column: AdvanceBio Peptide Plus
Sample: 10 peptide standard (5190-0583)
Injection: 3 µL
Flow rate: 0.5 mL/min
Mobile phase: A – 0.1%FA
B – 0.1% FA in ACN
% P
late
count
For Research Use Only. Not for use in diagnostic procedures.
8x 10
0
0. 5
1
1. 5
2
2. 5
3
3. 5
4
4. 5
5
5. 5
6
8x 10
0
0. 5
1
1. 5
2
2. 5
3
3. 5
4
4. 5
5
5. 5
6
C ounts v s. Acquisition Time (min)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
12
35
4
67
8
9 10AdvanceBio Peptide Mapping
AdvanceBio Peptide Plus
1
2
3 5
4
67 8
9
10
Column Options for Alternate Selectivity
25
10 Peptide Standard (p/n 5190-0583)
TIC
6. Renin substrate porcine
7. [Ace-F-3,-2 H-1] Angiotensinogen (1-14)
8. Ser/Thr Protein Phosphatase (15- 31)
9. [F14] Ser/Thr Protein Phosphatase (15-31)
10. Melittin (honey bee venom)
1. Bradykinin frag 1-7
2. Bradykinin
3. Angiotensin II (human)
4. Neurotensin
5. Angiotensin I (human)
0
0.02
0.04
0.06
0.08
0.1
0.12
0.14
0.16
0.18
FWH
M
Peptide peak
AdvBio Peptide Mapping
AdvBio Peptide Plus
Better
For Research Use Only. Not for use in diagnostic procedures.
mAb Peptide Mapping
26
LC/MS of mAb tryptic digest on 2.1 x 150mm AdvanceBio Peptide Plus Column
Hydrophilic peptide retention
Narrow Peaks with baseline resolution
Hydrophobic peptide elution
Reduced and fast analysis time
Critical and desired peptide mapping
components to achieve fast, selective,
and highly efficient peptide separations
across a wide dynamic range.
8 x10
0
1
2
3
4
5
Acquisition Time (min)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
Co
un
ts
Hydrophilic Hydrophobic
For Research Use Only. Not for use in diagnostic procedures.
LC/MS Peptide Map
27
sequence coverage 99.25% mass accuracy of 5 ppm
AdvanceBio Peptide Plus Column
For Research Use Only. Not for use in diagnostic procedures.
BioConfirm for Peptide Mapping
For Research Use Only. Not for use in diagnostic procedures.
28
MS spectrum MS/MS fragment spectrum
Biomolecules listb and y ion list
Sequence map
Chromatograms
AdvanceBio Peptide Plus Column
Identification of C-terminal Truncation
29
SLSLSPGK
SLSLSPG
For Research Use Only. Not for use in diagnostic procedures.
Analysis of Post-Translational Modifications
30
• Post-translational modifications (PTMs) on proteins such as monoclonal antibodies (mAb) are
critical quality attributes (CQA) that define drug efficacy and safety
• PTM containing peptides represent the minority of the tryptic mixture and often masked by more
dominant peptide signals
• Low stoichiometry & heterogeneity of many post-translational modifications make characterization
of modification sites challenging
• Advantage of high mass load tolerance of AdvanceBio Peptide Plus
• Comprehensive characterization of PTMs requires:
• Separation of native and modified peptides (Column)
• Sensitive detection (Mass Spectrometry)
• Robust LC/MS method
For Research Use Only. Not for use in diagnostic procedures.
Separation of Oxidized Peptides
31
5 x10
0
1
2
3
4
5
6
8
Acquisition Time (min)
4 5 6 7 8
7
Co
un
ts
Oxidized peptide
DLTMISR peptide
Relative % of Oxidation = 1.69% EIC
2x10
0
0.25
0.5
0.75
1
1.25
1.5
1.75
2
2.25
2.5
2.75
3
3.25
3.5
3.75
4
4.25
4.5
4.75
5
5.25
5.5
5.75
6
6.25
6.5
6.75
7
7.25
7.5
7.75
8
T74.0604
L,I86.0965
100.8496126.0552
144.0666
171.0775
175.1200
189.0863199.0725
b2217.0827
229.0918
245.1374
y2
262.1507
b3-H2O
312.1557
b3
330.1666
y3
375.2340
409.7209
443.1929
y4
506.2769
575.3696602.3394
y5
619.3600
619.6263
Counts v s. M ass-to-Charge (m/z)
60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 620 640 660
b4-H2Oy2 -NH3
y1
R
3x10
0
0.05
0.1
0.15
0.2
0.25
0.3
0.35
0.4
0.45
0.5
0.55
0.6
0.65
0.7
0.75
0.8
0.85
0.9
0.95
1
L,I
86.0960
88.0377
111.0555
144.0642
y1-NH3
158.0920
175.1176
189.0875
b2-H2O
199.0721
b2
217.0824
229.6381
y2
262.1503
286.1798
b3-H2O
312.1563
330.1614
351.6818
y3
375.2351
394.2188
417.2133
426.2170
458.2711
478.2066502.2897
y4
522.2694
571.3618
y5
635.3547
Counts vs. Mass-to-Charge (m/ z)
60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 580 600 620 640 660
DLTMISR
MS/MS spectra
Increase in mass (16Da)
Unmodified peptide
Unmodified peptide
Oxidized peptide
DLTMISR
AdvanceBio Peptide Plus Column
For Research Use Only. Not for use in diagnostic procedures.
Separation of Deamidated Peptides
32
ASQDVNTAVAWYQQKPGK peptide NTAYLQMNSLR peptide
Relative % of Deamidation = 0.21% – 15.9% Relative % of Deamidation = 9.1%
EIC
NT
AY
LQ
MN
SL
R 1
5.9
%
NT
AY
LQ
MN
SL
R 5
.5%
NT
AY
LQ
MN
SL
R
0.2
3%
NT
AY
LQ
MN
SL
R 0
.97
%
NT
AY
LQ
MN
SL
R
2.5
%
NT
AY
LQ
MN
SL
R
0.2
4%
NT
AY
LQ
MN
SL
R 0
.21
%
NT
AY
LQ
MN
SL
R
Deamidated peptides
non-d
eam
idate
dpepti
de
Deamidated peptide
Non-deamidated peptide
Deamidated peptide
Non-deamidated peptide
NTAYLQMNSLR
GFYPSDIAVEWESNGQPENNYK
Relative % deamidation = 9.1%
Relative % deamidation = 81.1%
ASQDVNTAVAWYQQKPGK
Deamidated peptide
Non-deamidated peptide
Relative % deamidation = 9.1%
ASQDVNTAVAWYQQKPGK
AdvanceBio Peptide Plus Column
For Research Use Only. Not for use in diagnostic procedures.
33
Traditional Silica AdvanceBio Peptide Plus Sub 2 µm
• Determination of deamidated peptides is an important goal of peptide mapping. Chromatographic resolution is important. MS/MS confirms which peak corresponds to which deamidation site.
• AdvanceBio Peptide Plus enhances analysis because it has higher selectivity for deamidated forms of peptide over the normal
form.
Separation of Deamidated Peptides
For Research Use Only. Not for use in diagnostic procedures.
VVSVLTVLHQDWLnGK or VVSVLTVLHqDWLNGK m/z 904.9984, doubly charged peptide
Sub 2 µm column requires
much higher back pressure to
achieve similar separation.
Traditional silica
columns don’t
resolve deamidation
as well as charged
surface columns.
Separation of Glycopeptides
34
EIC
G1F = 45.4%
G0F = 40.6%
G2F = 10.1%
G0 = 3.79%
Relative quantification
EEEQYNSTR peptide 3x10
0
0.5
1
1.5
2
3x10
0
1
2
3
4
5x10
0
0.2
0.4
0.6
0.8
1
1.2
5x10
0
0.2
0.4
0.6
0.8
1
4x10
0
0.2
0.4
0.6
0.8
1
1.2
Counts vs. Acquisition Time (min)
1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3 3.1 3.2
EEEQYNSTR
EEEQYNSTR+G0
EEEQYNSTR+G1F
EEEQYNSTR+G0F
EEEQYNSTR+G2F
Non-glycosylated BioConfirm results
Glycosylated
AdvanceBio Peptide Plus Column
For Research Use Only. Not for use in diagnostic procedures.
Pyro-
Glutamate
Deamidation
/Oxidation
Fragmentation
(Hinge)
Glycosylation
(G0, G1, G2)
Truncation
(Lys 0, 1, 2)
Disulfide
Shuffling
Aggregation
HILIC
IEC
IEC
IEC
RP
SEC
RP
LC/MS Intact mass
Fragment mass
Identification
PTM ID & locations
Glycan ID
Critical Quality Attributes & Testing Methods
Not just used for monoclonal antibodies – same techniques
are used for any potentially therapeutic protein
With a Multi-Attribute Method, peptide mapping can
monitor many of these CQAs simultaneously.
35
For Research Use Only. Not for use in diagnostic procedures.
Multi-Attribute Method (MAM)
36
0
5
10
15
20
25
30
35
40
45
50
G1F G0F G2F G0
% m
od
ific
atio
n
RP Heavy chain
HILIC
MAM (Pep Map)
0
0.2
0.4
0.6
0.8
1
1.2
1.4
1.6
1.8
% m
odifi
catio
n
%
G1F 44.8
G0F 44.7
G2F 8.9
G0 1.5
HILIC RP
Deamidations and Oxidation
monitored by the MAM (Pep Map)
Glycans monitored
Deamidation Oxidation
CEX
Comparison to traditional methods
For Research Use Only. Not for use in diagnostic procedures.
Choosing a Column Chemistry
For LC/MS work, AdvanceBio Peptide Plus with formic acid is the first choice.
Best peak shape with formic acid, high peak capacity, high mass load tolerance, excellent PTM resolution
(especially deamidation), peak shape and recovery of hydrophobic peptides, unique selectivity
Charged surface chemistry
AdvanceBio Peptide Plus
“Regular” silica chemistry
AdvanceBio Peptide Mapping
Eclipse Plus RRHD
ZORBAX 300
vs
37
For Research Use Only. Not for use in diagnostic procedures.
Exception 1: Sample is especially rich in small,
hydrophilic peptides.
Exception 2: Different selectivity is needed to separate
a key pair.
Poor retention of small, hydrophilic peptides is a feature common to
charged surface columns. In this case, try AdvanceBio Peptide
Mapping or Eclipse Plus C18 first.
Method Development Tips & Reminders
38
• Bonded Phase: C18 is routinely used. Try AdvanceBio Peptide Plus first; for alternate selectivity or highly
hydrophilic samples try AdvanceBio Peptide Mapping or a ZORBAX column.
• Column dimension: Good start with 2.1mm × 150mm, for higher resolution use longer column
• Gradient: Acetonitrile : Water with 0.1% formic acid, other organic solvent substitutions can be used for
different selectivity
Starting gradient time: 0-40% in 30min (1.3%/min)
• Temperature: Higher column temperature can dramatically improve both resolution and recovery (60 °C max)
• Desalt peptide mixture prior to injection
• Sample handling may cause artifacts (peptide modifications)
For Research Use Only. Not for use in diagnostic procedures.
Troubleshooting – Reasons for < 100% Sequence Coverage
Question to ask: Looking at the protein sequence, what’s missing?
• Very small and/or very hydrophilic peptides?
• If using AdvanceBio Peptide Plus, try AdvanceBio Peptide Mapping for better retention and/or
resolution.
• Very large and/or very hydrophobic peptides?
• Can you go to a higher percent organic mobile phase?
• Are peptides sticking to sample tubes or otherwise lost during sample preparation? Or on the LC?
• If using AdvanceBio Peptide Mapping, try AdvanceBio Peptide Plus
- May even need to consider a C8 column rather than C18
• Very large, or very small peptides of any hydrophobicity?
• Consider a different digestion enzyme
For Research Use Only. Not for use in diagnostic procedures.
39
More Information
Application Notes:
LC/MS Analysis of Peptide Mapping with
Formic Acid Ion-Pairing Agent
(5991-7574EN)
Enhancing the Quality of Peptide Mapping
Separation for the Analysis of Post-
Translational Modifications
(5991-7875EN)
How-to Guide
40
For Research Use Only. Not for use in diagnostic procedures.
Standards & Reagents
41
10 Peptide Standard (p/n 5190-0583) HSA peptides Standard
(p/n G2455-85001)
1. Bradykinin frag 1-7
2. Bradykinin
3. Angiotensin II (human)
4. Neurotensin
5. Angiotensin I (human)
6. Renin substrate porcine
7. [Ace-F-3,-2 H-1] Angiotensinogen (1-14)
8. Ser/Thr Protein Phosphatase (15- 31)
9. [F14] Ser/Thr Protein Phosphatase (15-31)
10. Melittin (honey bee venom)
7x 1 0
0
0 . 2
0 . 4
0 . 6
0 . 8
1
1 . 2
1 2 3 4 5 6 7 8 9 1 0 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 2 0 2 1 2 2 2 3 2 4 2 5
Co
un
ts
A cquisition Time (min)
1
23
5 67
10
9
8
4
Blank
1. AAFTE[CAM][CAM]QAADK
2. YLYEIAR
3. LVNEVTEFAK
4. KVPQVSTPTLVEVSR
5. RP[CAM]FSALEVDETYVPK
6. AVMDDFAAFVEK
7. HPYFYAPELLFFAK
Trypsin Digest Methylated BSA Standard
(p/n G1990-85000) Trypsin
For Research Use Only. Not for use in diagnostic procedures.
Summary
42
MS-compatible AdvanceBio Peptide Plus column delivers high peak capacity with sharp and narrow
peaks using MS-friendly formic acid modifier mobile phase conditions.
AdvanceBio Peptide Plus and AdvanceBio Peptide Mapping are superficially porous columns that yield
low back pressures & STM-like performance, allowing peptide mapping separations to be run on both
HPLC and UHPLC systems
Well-resolved PTM modified peptide peaks enabled reliable mAb peptide maps and development of
Multi-Attribute Methods
For Research Use Only. Not for use in diagnostic procedures.