Higher throughput glycosylation analysis of biopharmaceuticals by mass spectrometry

Transcription

1 Higher throughput glycosylation analysis of biopharmaceuticals by mass spectrometry Manfred Wuhrer Center for Proteomics and Metabolomics CASSS AT EUROPE, BARCELONA, MARCH 8, 18

2 GLYCOSYLATION Highly prevalent co and post translational protein modification (PTM) Considered to be the most complex PTM More than 5% of human proteins are glycosylated Why is analysis of glycosylation necessary? Protein protein interaction Recognition Signaling Trafficking Age dependent Changes with disease G.S.M. Kammeijer

3 GLYCOPROTEOMICS The most abundant monosaccharides in humans are: Glucose Da Galactose Da Mannose Da Fucose Da N Acetyl Dglucosamine Da N Acetyl Dgalactosamine Da N Acetylneuraminic acid Da 3 G.S.M. Kammeijer g.s.m.kammeijer@lumc.nl 3/1/18

4 ANALYSIS APPROACHES INTACT GLYCOPROTEINS GLYCOPEPTIDES RELEASED GLYCANS Different isoforms Protein specific Site specific Protein specific Analysis of complex samples Not site specific Requires isolated proteins Fast increase of complexity of the data Not site specific Not protein specific 4 G.S.M. Kammeijer g.s.m.kammeijer@lumc.nl 3/1/18

5 Workflow: MALDI TOF MS of N glycans Largely automated sample preparation Differentiation of sialic acid linkages Mild procedure: assessment of glycan modifications (e.g. acetylation, phosphorylation) Fast and largely automated data processing Can be combined with reducing end labeling, for CE-MS analysis or negative-mode MALDI-MS analysis 5 Insert > Header & footer 1 Mar 18

6 Ethyl esterification for differentiation and stabilization of sialic acid linkages α,6 OH EDC, EtOH, HOBt 1h at 37 C O +8.3 Da α,3 OH OH EDC, EtOH, HOBt O 1h at 37 C Da 6 1 Mar 18

7 PNGase F release under slightly acidic conditions Stimulating this reaction route by lowering the ph core GlcNAc aspartic acid peptide residue + carbodiimide reagent PNGase F core GlcNAc asparagine core GlcNAc glycosylamine carbodiimide coupled to core GlcNAc 7 Gerda Vreeker g.c.m.vreeker@lumc.nl 1 Mar 18

8 Automated cotton HILIC solid phase extraction 8 Cotton as HILIC microspe stationary phase: MHJ Selman et al. Anal Chem 11) 1 Mar 18

9 MALDI TOF MS spectrum of N glycans from human plasma Bladergroen/Reiding, 15, J. Proteome Res. 9 Insert > Header & footer 1 Mar 18

10 MALDI FTICR MS vs. MALDI TOF MS x1 4.5 MALDI TOF MS. Intensity x1 7 5 MALDI FTICR MS 4 Intensity m/z MALDI TOF MS MALDI FTICR MS Precision ±.1Da ±.1Da Sensitivity 85 glycans detected 11 glycans detected 1 Gerda Vreeker g.c.m.vreeker@lumc.nl 1 Mar 18

11 Data preprocessing: MassyTools Peak annotation on spectrum sums x m/z m/z Targeted extraction Area calculation of individual isotopes Subtract background from isotopes H5N5F1S Group isotopes Low total spectrum area in analytes Quality control ppm error Isotopic mismatch (quality score) Low fraction of analytes above S/N value Jansen BC, et al, 15, J. Proteome Res. 11 Insert > Header & footer expected observed 1 Mar 18

12 Repeatability 6% 5% 4% 3% % Day 1: plate 1 Day 1: plate Day 1: plate 3 Day : plate 4 Day 3: plate 5 MALDI FTICR MS plate Most abundant peak (H5N4E) Most abundant 1 peaks Intra plate plate 1 4.1% 9.% plate 4.8% 8.9% plate 3 4.4% 8.8% plate 4 4.% 9.6% plate 5 4.4% 8.5% Average all plates 4.3% 9.% Intra day (day 1) plate % 9.8% Relative area 1% % 7% 6% 5% 4% 3% % MALDI TOF MS Inter day plate % 9.9% plate Most abundant peak (H5N4E) Most abundant 1 peaks Intra plate plate 1 5.9% 15.3% plate 5.8% 17.1% plate 3 5.5% 14.% plate 4 4.8% 1.% plate 5 4.7% 15.8% Average all plates 5.3% 14.9% Intra day (day 1) plate % 14.% Inter day plate % 16.5% 1% % Glycan compositions

13 1% 9% 8% 7% 6% 5% 4% 3% % 1% % 1% 9% 8% 7% 6% 5% 4% 3% % 1% % Derived traits MALDI FTICR MS MALDI TOF MS TM THy TC CA CA3 CA4 CF CB CG CS AF A3F A4F AB AFB AFB AGS A3GS A4GS AFGS A3FGS A4FGS AFGS A3FGS A4FGS AGL A3GL A4GL AFGL A3FGL A4FGL AFGL A3FGL A4FGL AGE A3GE A4GE AFGE A3FGE A4FGE AFGE A3FGE A4FGE General Fucosylation Bisection Sialylation α,3 sialylation α,6 sialylation 13 Insert > Header & footer 1 Mar 18

14 INSTRUMENTATION CESI MS(/MS) 14 CE separates ions based on their electrophoretic mobility with the use of an applied voltage. ESI introduces protonated ions into the MS, the MS sorts and separates the ions according to their mass and charge in vacuum. Sciex CESI 8 Bruker MaXis Impact HD Center for Proteomics and Metabolomics

15 N GLYCAN ANLAYSIS WITH CESI MS N GLYCAN ANALYSIS CESI MS Sample PNGase F release Sample PNGase F release Dimethyl amidation Labeling CESI MS [ ] [1+] 15 G.S.M. Kammeijer g.s.m.kammeijer@lumc.nl 3/1/18

16 TPNG PROFILE WITH CESI MS BARE FUSED SILICA CAPILLARY Intens. x Time [min] Intens. x1 5 Injection: 5 psi 6sec 4 nl Time [min] BFS capillary 9 cm, 3µm id, BGE composition: 1 % AA, capillary coolant: C, voltage: kv, injection sample: 5 psi, 6 sec (4 nl) 16 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

17 TPNG PROFILE WITH CESI MS BARE FUSED SILICA CAPILLARY VS VS Intens. x1 5 Injection: 5 psi 6sec 4 nl Time [min] BFS capillary 9 cm, 3µm id, BGE composition: 1 % AA, capillary coolant: C, voltage: kv, injection sample: 5 psi, 6 sec (4 nl) 17 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

18 TPNG PROFILE WITH CESI MS BFS VS DYNAMIC COATED NEUTRAL CAPILLARY Intens. x1 6.8 Bare Fused Silica Capillary Injection: 5 psi 6sec (4 nl) Time [min] BFS capillary 9 cm, 3µm id,, BGE: 1 % AA, capillary coolant: C, voltage: kv, injection sample: 5 psi, 6 sec (4 nl) Intens. x Dynamic Coated Neutral Capillary Injection: 5 psi 6sec (4 nl) Time [min] Dynamic neutral coated BFS capillary 9 cm, 3µm id,, BGE: 1 % AA, capillary coolant: C, voltage: kv, injection sample: 5 psi, 6 sec (4 nl) 18 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

19 INCREASING SENSITIVITY OF GLYCAN/GLYCOPEPTIDE ANALYSIS WITH CESI MS 19 Significant increase in sensitivity with nano LC MS in combination with acetonitrile enriched nitrogen (DEN) gas ` Nitrogen gas coming in Nitrogen gas passes the headspace of the acetonitrile bottle Dopant enriched nitrogen gas is introduced in the ESI source Acetonitrile in bottle The solvent vapor acts as a dopant for enrichment. The charge state of multiple charged ions are modified optimizing the signal intensity. 19 Improvement factor of approximately one order of magnitude Application Note # LCMS 93 amazon speed ETD: Exploring glycopeptides in protein mixtures using Fragment Triggered ETD and CaptiveSpray nanobooster Kammeijer, G.S.M. et al. Anal. Chem., 16, 88 (11), pp /1/18

20 INCREASING SENSITIVITY OF GLYCAN/GLYCOPEPTIDE ANALYSIS WITH CESI MS Applicable on CESI MS? Kammeijer, G.S.M. et al. Anal. Chem., 16, 88 (11), pp /1/18

21 INCREASING SENSITIVITY OF GLYCAN ANALYSIS WITH CESI MS Background MS signal Intens. x A CESI MS Intens. x B Time [min]. x C CESI MS with DEN gas An overall lower background observed especially in the higher mass region Intens. x D Time [min] m/z 1 1 Kammeijer, G.S.M. et al. Anal. Chem., 16, 88 (11), pp /1/18

22 INCREASING SENSITIVITY OF GLYCAN ANALYSIS WITH CESI MS Improvement (total plasma N glycome) Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

23 INCREASING SENSITIVITY OF GLYCAN ANALYSIS WITH CESI MS Improvement (total plasma N glycome) 3x 3 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

24 GLYCOMICS LOD DETERMINATION Sample PNGase F release Derivatization α,3 N Acetylneuraminic acid α,6 N Acetylneuraminic acid VS Purification and enrichment Cotton HILIC Labeling Addition of label with cationic charge CESI MS analysis 4 Haan, de N., et al., Anal. Chem., 15, 87 (16), pp /1/18

25 LOD EXPERIMENTAL SET UP GLYCAN STANDARDS Dilution factor Dilution factor MALDI TOF MS MALDI TOF MS Volume µl Volume µl Dilution series Dilution series CESI MS CESI MS Injection volume 44 nl Injection volume 44 nl Concentration Amount used Concentration (addition of LE; 9:1) Injected amount Concentration Amount used Concentration Injected amount 6.39 pmol/µl 1.8 pmol 3.83 pmol/µl 169 fmol 1 1 fmol/µl fmol 9 fmol/µl 39.6 fmol 3. pmol/µl 6.39 pmol 1.9 pmol/µl 84.3 fmol 1 1 fmol/µl fmol 9 fmol/µl 3.96 fmol pmol/µl.56 pmol.77 pmol/µl 33.7 fmol 5 fmol/µl 1 fmol 45 fmol/µl 1.98 fmol 1.64 pmol/µl 1.8 pmol.38 pmol/µl 16.9 fmol 1 1 fmol/µl fmol 9 fmol/µl.396 fmol.3 pmol/µl.64 pmol.19 pmol/µl 8.4 fmol 5 fmol/µl 1 fmol 4.5 fmol/µl.198 fmol 5.13 pmol/µl.6 pmol.7 pmol/µl 3. fmol 1 1 fmol/µl fmol.9 fmol/µl.4 fmol 1.6 pmol/µl.13 pmol.4 pmol/µl 1.6 fmol.5 fmol/µl 1 fmol.45 fmol/µl. fmol 1.1 fmol/µl. fmol.9 fmol/µl.4 fmol CESI MS with DEN gas shows a ~1x higher sensitivity compared to MALDI TOF MS 5 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

26 TPNG PROFILE WITH CESI MS NEUTRALS Intens. x1 7. Dynamic Coated Neutral Capillary Injection: 5 psi 6sec (4 nl) Time [min] Dynamic neutrally coated BFS capillary, 9 cm 3µm id, BGE: 1 % AA, capillary coolant: 5 C, voltage: kv, injection sample: 5 psi, 6 sec (4 nl) Intens. x1 6 3 Static Coated Neutral Capillary Injection: 1 psi 6sec (9 nl) Time [min] Static neutrally coated BFS capillary, 9 cm 3µm id, BGE: 1 % AA, capillary coolant: 5 C, voltage: kv, injection sample: 1 psi, 6 sec (9 nl) 6 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

27 TPNG PROFILE WITH CESI MS NEUTRALS Intens. x1 7. Dynamic Coated Neutral Capillary Injection: 5 psi 6sec (4 nl) Time [min] Intens. x1 6 3 Static Coated Neutral Capillary Injection: 1 psi 6sec (9 nl) Time [min] 7 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

28 Intens. x1 6 3 x1 6 x1 6 x ZERO FLOW PRINCIPLE 1 min min 3 min x min Time [min] 8 Kammeijer, G.S.M. et al. Manuscript in preparation 3/1/18

29 EFFECT OF ZERO FLOW ON THE SEPARATION OF ISOMERIC N GLYCANS Intensx1 5.4 min Intensx min Intensx1 4 min Intensx min Time [min] Intensx min Time [min] Intensx Time [min] 1 min 1. VS HIGH MANNOSE. Intensx Intensx Time [min] min Time [min] 3 min VS GALACTOSYLATION. Intensx Intensx min min Time [min] Time [min] VS Intensx Intensx Time [min] min Time [min] 3 min VS. Intensx Time [min] 5 min. Intensx min Time [min] Intensx Time [min] 5 min Time [min] Time [min] Time [min]

30 EFFECT OF ZERO FLOW ON THE SEPARATION OF ISOMERIC N GLYCANS Intensx min Intensx min Intensx min BISECTION/GALACTOSYLATION Intensx1 4 Intensx1 4 Intensx min min min Time [min] Time [min] Time [min] VS VS. Intensx Intensx Intensx Time [min] 1 min Time [min] min Time [min] 3 min SIALYLATION. Intensx Intensx Intensx Time [min] 1 min Time [min] min Time [min] 3 min VS Intensx min Time [min]. Intensx Time [min] 5 min. Intensx min Time [min] Time [min] Time [min] Time [min]

31 31 GLYCOPEPTIDE / N GLYCAN ANALYSIS WITH CESI MS o o o o Glycan analysis in positive ionization mode is possible after derivatization and labeling CESI MS found to be ~1 times more sensitive than MALDI TOF MS Minor sample preparation is needed CESI MS shows great potential for characterization of N linked glycosylation in complex mixtures o Usage of static coated neutral capillary shows high potential for N glycan analysis o Isomeric separation visible for several N glycan species

32 Analysis of immunoglobulin G Fc variants (Beck et al., 1, American Chemical Society) get an integrated view of Fc modifications Middle down approach: focus on glycosylation of IgG allotypes interactions of the glycosylation with other post translational modifications (Vidarsson et al., 14, Frontiers in Immunology) 33 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

33 Middle down workflow Human plasma Allotypes IVIg CaptureSelect FcXL beads Incubate 1h shaking Wash and add buffer+ides Digest with IdeS O/N at 37 C Collect eluate Add FA to elute Fc Collect Fab in flowthrough Together with Govert Somsen, Andrea Gargano and Guusje van Schaick, VU University Amsterdam HILIC MS Dry samples in vacuum centrifuge Single Fc chains CESI MS (Bondt et al., 14, Molecular & Cellular Proteomics) 34 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

34 CESI MS of human plasma derived IgG Fc portions Single Fc chain from single donor human plasma.5 BPE 5 EIEs IgG1. 4 Intensity x Intensity x1 4 3 IgG.5 1 IgG4 IgG Time (min) Time [min] CE conditions: PEI coated capillary; BGE, % Acetic Acid + 1% MeOH; separation, kv, ⁰C 35 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

35 CESI MS of human plasma derived IgG Fc portions.5 BPE Donor 1 Subclass Nomenclature Allotype Position and amino acid Fc/ mass, G1F (non reduced + Lysine clipped) Theoritical Experimental (Da) mass mass Intensity x Time (min) IgG1 IgG IgG3 IgG IGHG1*3 E M V A IGHG* V A IGHG*6 M S IGHG3*6/7 V S K M K Q I R F IGHG3*16 V N N M K Q I R Y IGHG4*1 L R Intensity x BPE Donor IgG1 IgG IgG3 IgG IGHG1*3 E M V A IGHG1*7 D L V G IGHG* V A IGHG3*6/7 V S K M K Q I R F IGHG4*1 L R IGHG4* V R Time (min) Allotypes of single donor samples 36 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

36 HILIC MS of human plasma Donor 1 Donor 1. BPC 1.5 BPC Intensity x Intensity x Time [min] Time [min] Allotypes: IGHG1*3 IGHG1*3 & 7 IGHG* & 6 IGHG* HILIC conditions: amidehilic column; solvents, A: 98% ACN, % water,.1% TFA, B: 1% propanol, % ACN,.1% TFA 37 Thomas Senard, Guusje van Schaick, David Falck, Elena Dominguez Vega, Govert Somsen, Andrea Gargano 1/3/18

37 HILIC MS of human plasma Donor 1 Donor Intensity x EICs IGHG1*3 Intensity x EICs IGHG* IGHG1*3 IGHG1*7.5.5 IGHG* IGHG* Time [min] Time [min] Allotypes: IGHG1*3 IGHG1*3 & 7 IGHG* & 6 IGHG* HILIC conditions: amidehilic column; solvents, A: 98% ACN, % water,.1% TFA, B: 1% propanol, % ACN,.1% TFA 38 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

38 HILIC MS of IVIg 1.5 BPC Chinese BPC Dutch 1.5 IGHG1 IGHG 1.5 Intensity x Intensity x Lysine Time [min] Time [min] Chinese Dutch Intensity x IGHG1* IGHG1*1 IGHG*1 IGHG1* IGHG* IGHG* m/z 39 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

39 HILIC MS of IVIg 1.5 BPC Chinese IGHG1* Intensity x Intensity x Time [min] m/z 1.5 BPC Dutch 3 IGHG1*1 IGHG1* Intensity x Intensity x Time [min] m/z 4 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

40 HILIC MS of an allotype standard mab Fc portion IGHG1*3 Anti RhD, produced in HEK cells, purification via protein A/G affinity column.5 BPC GF+16 Da Intensity x1 4 Intensity x /GF+3 Da G1F+16 Da /G1F+3 Da GF+16 Da GF+3 Da Time [min] m/z 41 Thomas Sénard T.P.Senard@lumc.nl GF GF+16 Da GF+3 Da/G1F G1F+16 Da G1F+3 Da/GF GF+16 Da GF+3 Da Fc/ mass (non reduced + Lysine clipped) Theoritical mass Experimental mass (Da) /3/18

41 Conclusions MALDI MS of sialic acid stabilized glycans is powerful for the high sensitivity N glycosylation analysis of large numbers of complex samples. Sensitivity can be further boosted by approx. 1x by switching to CESI MS after a one pot reducing end labeling. Enhanced isomer separation is obtained with use of static neutrally coated capillaries and by initially applying a zero flow regime. Human IgGs show allotype and PTM diversity which can be resolved by CESI MS and HILIC MS of Fc portions For higher throughput glycomics analysis of complex samples it is important to have suitable data preprocessing methods that are fast, standardized and partially automated. 4 Thomas Sénard T.P.Senard@lumc.nl 1/3/18

42 ACKNOWLEDGEMENTS Center for Proteomics and Metabolomics Guinevere Kammeijer Thomas Senard Noortje de Haan Jan Nouta Sander Wagt Karli Reiding Gerda Vreeker Pablo Mohaupt Yuri van der Burgt Bas Jansen Simone Nicolardi Isabelle Kohler Elena Dominguez David Falck Andrea Gargano Guusje van Schaick Govert Somsen Gestur Vidarsson