Charged Surface Hybrid C18 for High Resolution LC and LC/MS Peptide Separations

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1 Charged Surface Hybrid C18 for High Resolution LC and LC/MS Peptide Separations Higher Quality Peptide Separations Using Hybrid Particle-Based Reversed-Phase Columns and CSH Technology Matthew Lauber, Ph.D. Senior Applications Chemist 2013 Waters Corporation 1

2 Reversed Phase Peptide Separations Peptide separations critically important peptide mapping, bottom-up proteomics reversed phase challenges remain LC performance MS performance TFA Ionic analytes peptides Secondary interactions - Poor peak shape Overloading at very low loads (<< neutrals) MS signal suppressing ion pairing agents needed TFA Peptide Still needed: high resolution, high sensitivity peptide separations regardless of eluent additive i.e. formic acid (FA) separations for LC-MS 2013 Waters Corporation 2

3 Charged Surface Hybrid 2013 Waters Corporation 3

4 Agenda The Peak Shape Problem Column Chemistries CSH Technology Peak Capacity CSH130 C18 and separations without TFA LC-MS of protein digests Small protein separations Peptide Mapping a Therapeutic mab CSH130 C18 for LC-UV-MS Disulfides and Deamidation Peptide Separation Technology (PST) Columns Quality control - QC tested with digests Analytical Standards and Reagents (ASR) 2013 Waters Corporation 4

5 The Peak Shape Problem 2013 Waters Corporation 5

6 Competitor s Industry Standard 5 µm m Porous Silica C % TFA Ion Pairing Strong 2.0 A % TFA 0.08% FA % FA Weak not detected Time (min) Competitor s Industry Standard C x 250 mm, Porous 5 µm, 300Å ACQUITY UPLC H-Class Bio 2% ACN for 1 min, then to 50% ACN over 60 min 0.3 ml/min 40 C 214 nm / Xevo G2 QTOF 5.6 µg MassPREP Peptide Mixture MassPREP Peptide Mixture Peptide Sequence 1 RASG-1 RGDSPASSKP 2 Angiotensin 1-7 DRVYIHP 3 Bradykinin RPPGFSPFR 4 Angiotensin II DRVYIHPF 5 Angiotensin I DRVYIHPFHL 6 Renin Substrate DRVYIHPFHLLVYS 7 Enolase T35 WLTGPQLADLYHSLMK 8 Enolase T37 YPIVSIEDPFAEDDWEAWSHFFK 9 Melittin GIGAVLKVLTTGLPALISWIKRKRQQ 2013 Waters Corporation 6

7 Ethylene Bridged Hybrid - BEH Technology U.S. Patent No. 6,686,035 B2 and others patent pending Bridged Ethanes In Silica Matrix Organo Silica Hybrid Particles ph stability Reduced ionic interactions Basis of Peptide Separation Technology EtO CH 2 CH 2 OEt OEt O Si Si Si O O Si O O Si O O Si O EtO OEt OEt Polyethoxysilane Et Et n EtO EtO OEt 4 EtO CH 2 Si + Si EtO OEt CH 2 Si OEt EtO EtO OEt Tetraethoxysilane Bis(triethoxysilyl)ethane Anal. Chem. 2003, 75, Waters Corporation 7

8 Small Particle Size Mobile Phase Peptides 1500 Da Peptide µm Porous Particle Diffusion-related band broadening Adsorption Equilibria H (mm) 1 Diffusion distances decrease Reduced Eddy diffusion Improved mass transfer kinetics 1.7 µm Column efficiency Narrower peaks 40 µl/min 2.1 mm ID 400 µl/min Velocity (mm/sec) 2013 Waters Corporation 8

9 Waters BEH130 C µm 3.0 Competitor s Industry Standard 5 µm C % TFA A % TFA 0.08% FA % FA Time (min) Time (min) Bridged Ethyl Hybrid BEH130 C18 Pore Size (Å) Ligand Waters ACQUITY UPLC BEH130 C x 150 mm, Porous 1.7 µm, 130Å EtO CH 2 CH 2 OEt O Si Si EtO Si O O O Si OEt O Si Si OEt O OEt O O Peptide Sequence 1 RASG-1 RGDSPASSKP 2 Angiotensin 1-7 DRVYIHP 3 Bradykinin RPPGFSPFR 4 Angiotensin II DRVYIHPF 5 Angiotensin I DRVYIHPFHL 6 Renin Substrate DRVYIHPFHLLVYS 7 Enolase T35 WLTGPQLADLYHSLMK 8 Enolase T37 YPIVSIEDPFAEDDWEAWSHFFK 9 Melittin GIGAVLKVLTTGLPALISWIKRKRQQ 2013 Waters Corporation 9

10 A New Column Chemistry CSH130 C % TFA A % TFA 0.08% FA 1.0 V o % FA Time (min) Waters ACQUITY UPLC CSH130 C x 150 mm, Porous 1.7 µm, 130Å Peptide Sequence 1 RASG-1 RGDSPASSKP 2 Angiotensin 1-7 DRVYIHP 3 Bradykinin RPPGFSPFR 4 Angiotensin II DRVYIHPF 5 Angiotensin I DRVYIHPFHL 6 Renin Substrate DRVYIHPFHLLVYS 7 Enolase T35 WLTGPQLADLYHSLMK 8 Enolase T37 YPIVSIEDPFAEDDWEAWSHFFK 9 Melittin GIGAVLKVLTTGLPALISWIKRKRQQ 2013 Waters Corporation 10

11 A New Column Chemistry CSH130 C18 Competitor s Industry Standard C18 Porous (300Å) 5 µm 2.1 x 250 mm Competitor s Superficially Porous Peptide C18 SPP (100Å) 1.7 µm 2.1 x 150 mm BEH130 C18 Porous (130Å) 1.7 µm 2.1 x 150 mm CSH130 C18 Porous (130Å) 1.7 µm 2.1 x 150 mm TFA UV absorbance (214 nm) Formic Acid Time (min) Time (min) Time (min) Time (min) 2013 Waters Corporation 11

12 Charged Surface Hybrid (CSH) Technology patent pending Charged Surface Hybrid (CSH) Technology and Its Use in Liquid Chromatography. P.C. Iraneta, K.D. Wyndham, D.R. McCabe, and T.H. Walter Waters White Paper EN 2011 Expands upon the robust BEH particle technology CSH130 C18 = BEH130 base particle + low level of basic moieties + trifunctional C18/end cap Acidic ph Positive Surface Charge Peptide 2013 Waters Corporation 12

13 Peak Capacity Peak Capacity = The number of peaks that can be separated within a retention window Neue, U. D., J Chromatogr A 2005, 1079 (1-2), The best metric for determining the quality of gradient separations 1 100% 9 peaks could resolve ~ Peak Height 50% 2.35σ w h 13.4% 4σ w 4σ 0% t gradient, t w h, 2013 Waters Corporation 13

14 Peak Capacity - FA vs TFA Competitor s Industry Standard Silica C18 5 µm 2.1 x 250 mm FA % TFA 0.00 % FA TFA Waters Corporation 14

15 Peak Capacity - FA vs TFA BEH130 C µm 2.1 x 150 mm Competitor s Industry Standard Silica C18 5 µm 2.1 x 250 mm FA % TFA 0.00 % FA TFA Waters Corporation 15

16 Peak Capacity - FA vs TFA Competitor s SPP Peptide C µm 2.1 x 150 mm BEH130 C µm 2.1 x 150 mm Competitor s Industry Standard Silica C18 5 µm 2.1 x 250 mm FA % TFA 0.00 % FA TFA Waters Corporation 16

17 Peak Capacity - FA vs TFA CSH130 C µm 2.1 x 150 mm 90% Competitor s SPP Peptide C µm 2.1 x 150 mm BEH130 C µm 2.1 x 150 mm 20% Competitor s Industry Standard Silica C18 5 µm 2.1 x 250 mm FA % TFA 0.00 % FA TFA Waters Corporation 17

18 MS Signal - FA vs TFA Peak Capacity MS Signal CSH130 C µm Competitor s SPP Peptide C18 1.7µm BEH130 C µm Competitor s Industry Standard Silica C18 5 µm FA % TFA 0.00 % FA TFA % TFA % FA FA TFA Waters Corporation 18

19 Loadability Attribute how much analyte can be loaded before peak shape deteriorates B Low Mass Load 0.6 µg of mixture Low Mass Load CSH130 CSH C18 C µm BEH C A Typical Mass Load 6 µg of mixture High Mass Load *Previously shown CSH C18 BEH C18 CSH130 C µm 350 BEH130 C µm 350 P c,4σ 300 P c,4σ 300 BEH130 C µm P c4σ % TFA % FA TFA FA Percent 0.05TFA % TFA % FA % TFA % FA TFA FA Percent 0.05TFA Waters Corporation 19

20 CSH130 C18 and Separations without TFA 2013 Waters Corporation 20

21 LC-MS 2E+6 Enolase Tryptic Digest CSH130 C µm T6 0.1% FA Wh,avg= 4.0 s Intensity T38 T14 Pc,4σ = 532 T51 T23 1E+6 T35 T42 T45 T40 T27 T37 T10 0.1% TFA 0E Waters ACQUITY UPLC CSH130 C x 150 mm, 1.7 µm, 130Å 2% ACN for 1 min, then to 50% ACN over 60 min 0.3 ml/min 40 C 2013 Waters Corporation 31 Time(min) x drop in sensitivity ACQUITY UPLC H-Class Bio Xevo G2 QTof 500 pmol MassPREP Enolase Digest p/n

22 CSH130 C18 vs Other Chemistries Intensity 2E+6 0.1% FA BEH130 C µm BEH C µm P = 399 Pc,4σ c,4σ = 399 1E+6 0E+0 Intensity 2E Competitor s Superficially Porous Competitor A Peptide C µm Superficially Porous C µm = PPc,4σ c,4σ = 1E+6 0E Intensity 2E Time(min) CSH130 C CSH C µmµm P = 532 Pc,4σ c,4σ = 532 1E+6 0E Time(min) Improvement for both optical and MS detection 2013 Waters Corporation 22

23 LC-MS Retention and Selectivity 1E+6 BEH130 C18 T3 SVYDSR T12 ANIDVK T19 HLADSK T10 GVLHAVK T40 IATAIEK More positive charge T3 T12 T19 T10 T40 0E E+6 Competitor s Superficially Porous Peptide C18 Intensity T3 T12T10 T19 T40 0E E+6 CSH130 C18 T10 T19 T12 T3 T40 0E Time(min) 2013 Waters Corporation 23

24 Large Peptides/Small Proteins 0.1% FA Peptide/Protein kda 1 Bradykinin Å A CSH130 C µm BEH130 C µm Time (min) Renin Substrate Ubiquitin Cytochrome C (Equine) Insulin (Bovine) Melittin A Å A BEH300 C µm Time (min) x 150 mm columns 2% ACN for 1 min, 0.8 then to 50% ACN over 60 min ml/min C ACQUITY UPLC H-Class Bio 214 nm / Xevo G2 QTOF 1 µg each component Time (min) 2013 Waters Corporation 24

25 Peptide Mapping of a Therapeutic mab 2013 Waters Corporation 25

26 Peptide Mapping a Therapeutic mab Trastuzumab (Herceptin; Genentech) Breast Cancer, Anti-HER2 One of the highest grossing therapeutic mabs (~5 billion $/yr) Biosimilars Basis for a new antibody drug conjugate (ADC; Trastuzumab emantansine) o Phase III clinical trials completed High peak capacity at mass loads to detect trace modifications and thoroughly characterize o o o o o Disulfide linkages Deamidation Oxidation Glycosylation Conjugation in ADCs JCO 2010;28: Waters Corporation 26

27 Non-Reduced Lys-C C Peptide Mapping Non-Reduced Lys-C Digests Minimal complexity + disulfides preserved 27 different linear peptides 8 different disulfide linked peptides 150 to 11,000 Da A recent Amgen protocol: Anal Biochem 2011, 411 (2), L: Lys-C Cleavage (C-terminal Side of Lys) H: H: L: Disulfide Bond Light Chain Heavy Chain 2013 Waters Corporation 27

28 Method Considerations ACQUITY UPLC BEH130 C18 1.7µm ACQUITY UPLC CSH130 C18 1.7µm 2.1 x 150 mm % TFA 0.08% FA Optimize peak capacity Small compromise to MS Sensitivity Elevated Temperature (60 C) Improved peak shape and recovery 5-11 kda species 350 CSH130 C kda Species BEH130 C C Peak Capacity BEH130 C C 200 MS Signal Percent TFA Other applications of elevated temp. Anal Chem 2011, 83 (15), Anal Biochem 2011, 411 (2), MAbs 2010, 2 (4) J Biol Chem 2009, 284 (51), Waters Corporation 28

29 Non-Reduced Lys-C C Peptide Maps Trastuzumab BEH130 C18 Peak Capacity = % Coverage 0.02% TFA 0.08% FA 5 A A CSH130 C18 Peak Capacity = % Coverage 4 5 wh (sec) Peak BEH130 C18 CSH130 C Time (min) 2013 Waters Corporation 29

30 LC-UV UV-MS with an MS-Compatible Mobile Phase CSH130 C18 Low TFA mobile phase 0.02% TFA 0.08% FA MS Optimized Peak Capacity + MS signal UV signal ACQUITY H-Class Bio CSH130 C µm UV Peak Area MS UV UV Detector ESI-MS Xevo G2 QTof m/z Waters Corporation 30

31 Disulfide Characterization H: x H: L:1-42 x L: H:1-30 x H: H: x H: L: x L: H x H: A210 Non-Reduced L: x H: H: x H: CSH130 C18 - Optimized Gradient Blank Reduced H:1-30 H: H: L: H: L: H: L: H H: L: H: L: A Time (min) 2013 Waters Corporation 31

32 Assaying Deamidation CSH130 C18 - Optimized Gradient 44 GLEWVARIYPTNGYTRYADSVK 65 Binding region from the heavy chain Prone to deamidation 0.5 A H:44-65 * * 92 % Asn 7 % isoasp 1 % Asp Unmodified Deamidated Intensity 3E+5 0E E Mass shift Da * 0E E * Time (min) 0E m/z 2013 Waters Corporation 32

33 Conclusions CSH130 C18 Peptide Separations Improved loadability and greater peak capacity vs. other C18 columns Excellent peak shape with both TFA and FA mobile phases (highly compatible with MS) 130Å pore size optimal for species up to 8-10 kda Unique selectivity (basic residues) o Less retentive Exceptional chemistry for peptide separations Peptide mapping... proteomics and peptide isolation 2013 Waters Corporation 33

34 Peptide Separation Technology Columns 2013 Waters Corporation 34

35 New Addition to the Suite of Waters Peptide Separation Technology Peptide Separation Technology Peptide C18 Columns QC Tested with Digests BEH Technology BEH130 C18 and BEH300 C18 Industry Leading Performance for Most Applications Two Pore Sizes Particle Sizes: 1.7 µm, 3.5 µm, 5 µm Analytical, Nano and Prep Columns Now even more tools in the toolbox CSH Technology CSH130 C18 Best columns for formic acid separations Unique selectivity 2013 Waters Corporation 35

36 UPLC and HPLC CSH130 C x150 mm 1.7 µm A High peak capacity separations not limited to UPLC 0.1 % FA ~8000 psi CSH130 C18 Peptide Separation Technology Columns A % TFA 0.2 Available 0.0 Now: Upcoming: Method Analytical Columns 1.0 Time (min) Nano (75, 150, 1.0 Time 300 (min) µm ID) Transfer 1.7 µm Prep Columns (5 µm) 2.5 µm XP Longer Run Time Lower Pressure µm XP µm A Time (min) ~3000 psi A Time (min) 2013 Waters Corporation 36

37 Quality Control CSH130 C % Formic Acid 2013 Waters Corporation 37

38 Quality Control CSH130 C18 Batch-to-Batch Reproducibility Cytochrome C Digest, 0.1% Formic Acid Each new column will perform comparably to one previously used AU AU AU AU Batch 110 T1 T13-T14 T Minutes Batch Minutes 8.00 Batch Minutes 8.00 Batch 102 T4 T9-T Minutes 8.00 *Data provided by S. McCall/P. Iraneta 2013 Waters Corporation 38 T10 T8 T15 T19C T19 T12-T13 T12

39 Analytical Standards and Reagents (ASR) MassPREP Peptide Mixture Digestion Standards Cytochrome C Digestion Standard Part Number: Rapigest SF Amgen Digestion Protocol Anal Chem (4): Waters Corporation 39

40 Useful Literature Charged Surface Hybrid (CSH) Technology and Its Use in Liquid Chromatography P.C. Iraneta, K.D. Wyndham, D.R. McCabe, and T.H. Walter Waters White Paper EN 2011 Increasing Peak Capacity in Reversed Phase Peptide Separations with Charged Surface Hybrid (CSH) C18 Columns M.A. Lauber, S.M. Koza, K.J. Fountain Waters Application Note EN 2013 Peptide Mapping and Small Protein Separations with Charged Surface Hybrid (CSH) C18 and TFA-Free Mobile Phases M.A. Lauber, S.M. Koza, K.J. Fountain Waters Application Note EN 2013 High Resolution Peptide Mapping Separations with MS-Friendly Mobile Phases and Charge Surface Modified C18 M.A. Lauber, S.M. Koza, S.A. McCall, B.A. Alden, P.C. Iraneta, and K.J. Fountain Manuscript in Preparation Waters Corporation 40

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