mass spectrometric analysis of...

Mass Spectrometric Analysis of Glycans

Techniques in Glycobiology Hui Zhang

October 21, 2013


• Mass spectrometric analysis • Preparation of glycans for

analysis

March 26, 2014 2

Structure and Names of Common Monosaccharide

Varki, A. e. a., Essentials of Glycobiology. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 1999.

CFG and Essentials for Glycobiology

Biatennary Sialoglycan

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8

Major Classes of N-Glycans

Essentials of Glycobiology

Second Edition

Glycan Mass Cacula@on

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=(162.0528*3+203.0794+221.0899+22.9898)+146.0579*F+203.0794*N+162.0528*H+291.0954*A+22.9898*A-1.0078*A

=F2+G2*E2-22.9898*E2

March 26, 2014 10

PNGase F Released N-Glycans

Fetuin Glycans without Modificaiton

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%Int.

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13 mV[sum= 1309 mV] Profiles 1-100 Unsmoothed -Baseline 60

8.4.6a MS2 High Mass Gate Calibration Using ACTH(18-39)Data: punit\31jan\Fetuin Aniline power 95_2000_20001 1 Feb 2012 12:58 Cal: shadi_Nov3 3 Nov 2011 9:27 Shimadzu Biotech Axima Resonance 2.9.1.2.20100505: Mode positive, High 2000+, Power: 95

2653.5548{sn18}2340.6459{sn18}

2654.5462{sn16}

2966.4317{sn13}2339.6692{sn13}

2028.7383{sn12}

2341.6893{sn10} 2967.4612{sn9}2652.5462{sn9}

2288.6335{sn8}2026.7573{sn7}2968.3971{sn7}2342.6703{sn7}

2655.5447{sn6}2203.5944{sn6} 2516.4966{sn6}

2969.3603{sn5}2187.6296{sn4}

Matrix DHB +DMA


March 26, 2014 12

=(162.0528*3+203.0794+221.0899+22.9898)+146.0579*F+203.0794*N+162.0528*H+291.0954*A+22.9898*A-1.0078*A


0

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%Int.

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2653.5548{sn18}2340.6459{sn18}

2654.5462{sn16}

2966.4317{sn13}2339.6692{sn13}

2028.7383{sn12}

2341.6893{sn10} 2967.4612{sn9}2652.5462{sn9}

2288.6335{sn8}2026.7573{sn7}2968.3971{sn7}2342.6703{sn7}

2655.5447{sn6}2203.5944{sn6} 2516.4966{sn6}

2969.3603{sn5}2187.6296{sn4}

+4Na-3H

+3Na-2H +2Na-H

+Na

Matrix DHB +DMA

GlycoWorkbench •  A soDware tool developed by the EUROCarbDB ini@a@ve

•  Assist the manualinterpreta@on of MS data •  Provides an easy to use graphical interface, a comprehensive and increasing set of structural cons@tuents an exhaus@ve collec@on of fragmenta@on types, and a broad list of annota@on op@ons

•  A. Ceroni, K. Maass, H. Geyer, R. Geyer, A. Dell and S.M. Haslam, GlycoWorkbench: A Tool for the Computer-‐Assisted Annota<on of Mass Spectra of Glycans, Journal of Proteome Research, 7 (4), 1650-‐-‐1659, 2008, DOI: 10.1021/pr7008252

March 26, 2014 14

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GlycoWorkbench


• Mass spectrometric analysis • Preparation of glycans for

analysis

March 26, 2014 16

Site Specific Glycan Analysis

N

N

S

N

G Q M P

S S

S

S Q

T

T

V

A C L G

I C H

E

R

K

R

S K

G

E

A F D Y

P

P

M L

W

I

(75%) (25%)

Site Mapping and Characterization

N

N

S

N

G Q M P

S S

S

S Q

T

T

V

A C L G

I C H

E

R

K

R

S K

G

E

A F D Y

P

P

M L

W

I

Characterization of Glycoproteins and Glycans Using MS

Glycoproteinsx

Pep@des +Glycopep@des

Formerly glycosylated pep@des + Glycans

Formerly glycosylated pep@des

Glycans

Proteolysis

Release glycans

Ioniza@on

Detector

Ion trap

Sample plate

Analyzer

Fragmenta@on

Separa@on

Sample preparation procedure MALDI-MS-MSn

•  Glycan extrac@on

•  Poten@al issues –  Non-‐specific binding –  Sample loss (affinity; mul@ple purifica@on) –  Difficulty to remove reagents aDer deriva@za@on (sialic acid modifica@on:

reagents severely interfere glycan ioniza@on)

Current methods

Enzyme

C18/C8 Carbo modify Carbo MS

S. Yang and H. Zhang, Proteomics Clin. Appl. 2012, 11-12, 596-608

Immobiliza@on on solid-‐phase: Immobiliza@on in pH 10 on N-‐terminus and lysine

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Protein digestion (optional)

Conjugation of proteins to beads

Release of glycans

Complex biological samples

Glycoprotein Peptide Glycan Non-glycoprotein Glycopeptide Solid bead with aldehyde group

Beads and peptides

Glycans

S. Yang et al., Anal. Chem. 2013, 85(11), 5555-5561.

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2865.8

2865.8

NH2-Lys-Val-Ala-Asn-Lys-Thr-COOH

NH2-Lys-Val-Ala-Asn-Lys-Thr-COOH

a

b

Conjuga@on of glycopep@de to solid support

Conjuga@on of glycopep@de to solid support at different @me

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Supplementary Figure 1: Conjugation of glycopeptide to solid support at different coupling time.

Rel

ativ

e in

tens

ity o

f un-

coup

led

SG

P in

sol

utio

n

Coupling time (hour)

Glycan Release

•  Enzyma@c release of N-‐glycans •  β-‐elimina@on for O-‐linked glycans •  Proteases: Glycans can be obtained nonselec@vely by degrada@on of the protein by proteases to generate glycopep@des.

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PNGase F Released N-Glycans

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Chapter 47, Figure 2

Glycosidases Used for Structural Analysis

Essentials of Glycobiology Second Edition

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P-toluidine modified Sialic Acid Glycans on Solid-phase

Release of Glycans from Solid Support at Different Time

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Supplementary Figure 2: Release of glycan from solid support at different time.R

elat

ive

inte

nsity

of r

elea

sed

glyc

an in

sol

utio

n

Release time (hour)

GIG (chemoselec@ve method) Glycoprotein Immobilization for Glycan Extraction

(GIG)1

1S. Yang et al., Anal. Chem. 2013, 85(11), 5555-5561. 2P. Shah, S. Yang et al., Anal. Chem. 2013, 85 (7), 3606-3613.

3G.J. Rademaker et al., Anal. Biochem. 1998, 257, 149-160.

immobilize modify2

enzyme

β-elimination3

MS

wash

MS

Analysis of Sialylated glycans

•  Sialic acid are nine carbon containing acidic monosaccharides

•  Sialic acids are typically found at

the terminal residue of N-glycans, O-glycans, and glycosphingolipids

•  Sialic acids play crucial role in cell

surface interactions, protect cells from membrane proteolysis, help in cell adhesion, determine half life of glycoprotein in blood

Comparative Serum Glycoproteomics Using Lectin Selected Sialic Acid Glycoproteins with Mass Spectrometric Analysis: Application to Pancreatic Cancer Serum Journal of Proteome Research 2006, 5, 1792-1802

Mass Spectrometry of Sialic Acid

•  N-glycans are analyzed using MALDI

•  Sialic Acid are negatively charged

•  Sialic acid residues of sialoglycans are labile to the ionization process of MALDI TOF –  Insource Decay (labile carboxylic proton) –  Post Source Decay

(Matrix / LASER/ Detection Mode)


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%Int.

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2653.5548{sn18}2340.6459{sn18}

2654.5462{sn16}

2966.4317{sn13}2339.6692{sn13}

2028.7383{sn12}

2341.6893{sn10} 2967.4612{sn9}2652.5462{sn9}

2288.6335{sn8}2026.7573{sn7}2968.3971{sn7}2342.6703{sn7}

2655.5447{sn6}2203.5944{sn6} 2516.4966{sn6}

2969.3603{sn5}2187.6296{sn4}

+4Na-3H

+3Na-2H +2Na-H

+Na

Matrix DHB +DMA

v

coupling

P-toludine

PNGaseF

Trypsin

MALDI MS LC MSMS

Shimadzu AXIMA Resonance PK Shah, S Yang, S Sun, P Aiyetan, KJ Yarema, and H Zhang. Mass Spectrometric Analysis of Sialylated Glycans Using Solid Phase Labeling of Sialc Acids. Analytical Chemistry (2013)


March 26, 2014 37

=(162.0528*3+203.0794+221.0899+22.9898)+146.0579*F+203.0794*N+162.0528*H+291.0954*A+22.9898*A-1.0078*A

=Glycan Mass+p-tolu*A-22.9898*A

March 26, 2014 38


P-toluidine modified Fetuin Glycans

100

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20

0 2000 2200 2400 2600 2800 3000 3200 3400 3600


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%Int.

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2653.5548{sn18}2340.6459{sn18}

2654.5462{sn16}

2966.4317{sn13}2339.6692{sn13}

2028.7383{sn12}

2341.6893{sn10} 2967.4612{sn9}2652.5462{sn9}

2288.6335{sn8}2026.7573{sn7}2968.3971{sn7}2342.6703{sn7}

2655.5447{sn6}2203.5944{sn6} 2516.4966{sn6}

2969.3603{sn5}2187.6296{sn4}

+4Na-3H

+3Na-2H +2Na-H

+Na

Matrix DHB +DMA

Reported N-‐glycans from Fetuin

Solid-phase permethylation of glycans for mass spectrometric analysis Rapid Commun Mass Spectrom. 2005 ; 19(23): 3421–3428

Coupling

p-toluidine

PNGaseF/Trypsin

MALDI MS

Protein Amino Link Beads

P-Toluidine

P-Toluidine Heavy

Glycan LC-MS/MS

p-Toluidine-d9

Isotopic Labeling of Sialic Acids

Punit Shah et al. Analytical Chemistry. 2013

Serum Glycan Mixed 1:1 Light to heavy

Quantitation of Sialoglycans

Advantages of Solid Phase Glycan Extraction

•  Reduce glycan processing steps •  Modifica@on of glycans by enzymes or chemicals •  Quan@ta@ve analysis of glycans and glycoproteins •  The modifica@ons of sialic acids stabilize sialylated glycans

•  Increase the ioniza@on by increase hydrophbicity and removing nega@ve charge from glycans

•  The label P-‐toludine is hydrophobic and allows reten@on on C18 columns •  The difference between the pair helps

–  Determina@on of number of sialic acid –  Iden@fica@on of glycans –  Quan@ta@on of sialylated glycans

•  Sample is first bound to the beads and hence the proteins aDer removal of N glycans can be analyzed using Tryp@c diges@on

•  Along with Sialic acid Aspar@c acid and glutamic acid get modified and can be used for pep@de/protein Quan@ta@on

Glycan Fragmentation Ions

March 26, 2014 45

Joseph Zaia Mass Spectrometry and the Emerging Field of Glycomics. Chemistry & Biology (2008) 15, 881–892.

Domon and Costello, 1988

March 26, 2014 46


March 26, 2014 47

Glycan Structures •  Glycans are usually cons<tuted by different

monosaccharide units. •  These monosaccharide units are covalently linked by

glycosidic bonds, either in α or β or configura<on depending on the orienta<on of the anomeric centers.

•  Glycans can have complex structures with mul@ple branching points, since each hydroxyl group of a monosaccharide cons@tutes a possible point of forma@on for a glycosidic bond.

•  Further modifica@ons of the basic monosaccharide unit at the various hydroxyl posi@ons, such as subs@tu@on of the proton with other moie@es or deoxygena@on, contribute to the structural complexity.

March 26, 2014 48

Mass Spectrometry of Glycans •  Mass spectrometry is the main analy@cal technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensi@vity and the ability to handle the complex mixtures of different glycan varia@ons.

•  Modern MS techniques are capable of producing mass spectra of both the whole glycan (molecular ion) and the fragmented glycan (fragment ions).

•  The high level of sequence informa@on contained in the fragment ion spectra can be exploited to resolve the structure of a glycan molecule.

March 26, 2014 49

Automated InterpretaDon of Mass Spectrometry Data

•  the current status of tools to analyze glycan MS data shows that automated interpreta@on of mass spectrometric data is s@ll an evolving field. Up to now, only a few soDware tools have been available to support experimentalists during the annota@on process, and the capability of these tools is somewhat varied.

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Automated InterpretaDon of Mass Spectrometry Data

•  Library-‐based sequencing tools iden@fy the glycan sequence by matching the unassigned mass spectra with data derived from known glycan structures.

•  Similarly to the SEQUEST method used for protein sequencing, GlycosidIQ8 generates a theore@cal peak list for each structure in the database by compu@ng all its theore@cal fragments. The best match between the theore@cal peak lists and the mass spectra is then derived using a suitable scoring func@on.

•  Both approaches are severely limited by the availability of reliable data, since no comprehensive and well-‐curated collec@on of experimentally derived glycan sequences exists at the moment, and no public collec@on of assigned MSn spectra from pure glycans is available.

March 26, 2014 51

De novo sequencing tools from MS data

•  GlycoMod, Glyco-‐Peakfinder, and Cartoonistuse data from MS measurements to es@mate the quan@@es and classes of monosaccharide components of the glycan structure.

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de novo sequencing from MSn

•  STAT , Oscar, StrOligo, GLYCH generate all the possible structural topologies from a composi@on selected by the user among those compa@ble with the precursor mass.

March 26, 2014 53

Computer-‐Assisted InterpretaDon of MS Data

•  Expert knowledge about glycan biosynthesis is fundamental for the correct interpreta@on of a spectrum.

•  EUROCardDB: databases, bioinforma@cs tools, glycobiology, glycomics.

•  GlycoWorkbench assist the manual interpreta@on of MS data. GlycoWorkbench is to evaluate a set of structures proposed by the user by matching the corresponding theore@cal list of fragment masses against the list of peaks derived from the spectrum.

•  GlycanBuilder enables a rapid assembly of structure models using a comprehensive collec@on of building blocks, and their display in several popular symbolic nota@ons.

•  The in silico fragmenta<on engine computes a complete list of theore@cal fragments including mul@ple glycosidic cleavages and all the possible ring fragments for every available type of monosaccharide.

March 26, 2014 54

Glycomics Using Tandem Mass Spectrometry

•  Assignments can be confirmed in a second experiment employing ESI-‐MS/MS instrumenta@on by selec@ng each molecular ion for collisional ac@va@on and recording its fragment ion spectrum.

•  Addi@onal informa@on can be provided by MS experiments on chemical and enzyma@c digests, the choice of which is guided by the sequence informa@on provided by mass mapping and MS/MS experiments.

March 26, 2014 55

Linkage Analysis •  The principle of this method is to introduce a stable subs@tuent (an ether-‐linked methyl group) onto each free hydroxyl group of the na@ve glycan.

•  The linkages, which are much more labile than the ether-‐linked methyl groups, are then cleaved with free hydroxyl groups at the posi@ons that were previously involved in a linkage.

March 26, 2014 56

Glycan Permethyla@on •  Although MALDI-‐MS structural analysis of most glycans can basically be performed in their na@ve forms.

•  Determina@on of branching, interglycosidic linkages and the presence of configura@onal and conforma@onal isomers need permethyla@on.

•  Permethyla@on stabilizes glycans, yielding more predictable ion products when subjected to MS/MS experiments.

•  Permethylated glycans ionize more efficiently than their na@ve counterparts.

March 26, 2014 57 Ciucanu I, Kerek F. Carbohydr. Res. 1984; 131: 209.

Permethyla@on of Glycans •  Permethyla@on of glycan-‐ OH→OMe

–  Addi@on of MeI •  Analyzed permethylated glycans by applying MSn fragmenta@on as

needed to completely determine the structure

March 26, 2014 58 J. Am. Chem. Soc. (2003) 125(52): 16213-9.

BSA-OGlcNAcpepmix-2nmol-CID-ETD-HCD #5157 RT: 44.73 AV: 1 NL: 4.53E6T: FTMS + c NSI d Full ms2 [email protected] [100.00-1325.00]

100 200 300 400 500 600 700 800 900 1000 1100 1200 1300m/z

0

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30

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45

50

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Re

lativ

e A

bu

nd

an

ce

MH, 1313.48

y11, 1216.61

y10, 1129.55

MH-‐He

xNAc

,1110.58

y9, 1030.51

y11-‐He

xNAc

, 1013.54

y10-‐He

xNAc

, 926.50

y9-‐HHe

xNAc

, 827.43

b7, 827.43

y8-‐HexNAc

, 730.38

MH+

2 , 657.83

y7-‐HexNAc

, 631.31

MH-‐He

xNAc

+2, 555.80

y6, 544.28

y7, 834.40

S+HexNAc Δ290.12m/z

y5, 487.26 y10-‐He

xNAc

+2, 463.75

y9-‐HexNAc

+2, 414.22

y3, 329.19

b3, 284.16

b3-‐H

2O, 266.15

HexN

Ac+1, 204.09

HexN

Ac-‐H

2O+1, 186.07

b2-‐H

2O, 167.08

HexN

Ac-‐66+

1 , 138.05

He

xNAc

-‐78+

1 , 126.05

PSVPV S GSAPGR

y6

y7

GlcNAc

HexN

Ac-‐60+

1 , 144.06

HCD spectra

204.084 HexNAc+1

[C8H14O5N]+ 186.075

[C8H12O4N]+ 168.064

[C8H10O3N]+

144.064 [C6H10O3N]+

138.054 [C7H8O2N]+

126.054 [C6H8O2N]+

HCD (zoomed in) D

PGGSTPVSSANMM

GlcNAc

b2,

154.

548

201.

858

179.

024

172.

741

122.

112

239.

007

110 130 150 170 190 210 230 250 m/z

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Rel

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The Informatics Challenges of Diverse Glycomic Data

•  Efforts to correlate large data sets obtained from glycomic,

transcriptomic, genomic, and proteomic studies have met with several challenges.

•  Representa@on of glycan chemical structures is difficult because of their complexity and branching panerns. The use of single alphabet codes, as employed to describe nucleic acid and amino acid sequences, is not applicable to glycans.

•  The field is in need of a comprehensive bioinforma@cs plaoorm that stores, integrates, and processes data from glycomic and other “omic” studies and disseminates them in a meaningful fashion via the Internet to the scien@fic community.

March 26, 2014 61

Databases and Bioinformatics Platforms

•  GlycoSuiteDB, Sweet, KEGG GLYCAN •  The Consor@um for Func@onal Glycomics (CFG) •  EuroCarbDB •  Na@onal Center for Glycomics and glycoproteomics •  Glycomod: all possible composi@ons of a glycan structure •  GlycoPep DB: N-‐glycopep@de composi@onal assignment •  Cartoonist: automated annota@on of N-‐glycan MALDI TOF mass

spectra with cartoons represen@ng the most plausible glycan assemblies synthesized by mammals using 300 manually determined archetypes.

March 26, 2014 62

Databases and Bioinformatics Platforms

•  Peptoonist: automated iden@fica@on of N-‐glycopep<des using a combina<on of MS and MS/MS data

•  Glyco-‐Peakfinder: rapid assignment of glycan composi@ons, is intended to be en@rely a de novo plaoorm for composi@onal analysis

•  SysBioWare: carbohydrate assignment •  NCRR GlycomicsPortal •  SimGlycan •  Accurate Glycan Analyzer •  GlycoWorkbench •  Byonics’s glycopep@de search Engine

March 26, 2014 63

What GlycoWorkbend does •  GlycoWorkbench is a suite of soDware tools designed for the rapid

drawing of glycan structures and for assis@ng the process of structure determina@on from mass spectrometry

•  data. The graphical interface of GlycoWorkbench provides an environment in which structure models can be rapidly assembled, their masses can be computed, their fragments

•  can be automa@cally matched with MSn data, the results can be compared to assess the best candidate, and, finally, the best match to the spectrum can be displayed graphically.

•  GlycoWorkbench can greatly reduce the @me needed for the interpreta@on and annota@on of mass spectra of glycans. The aim of GlycoWorkbench is to offer complete support

•  for the rou@ne interpreta@on of MS data.

March 26, 2014 64

GlycanBuilder

•  Damerell D, Ceroni A, Maass K, Ranzinger R, Dell A, Haslam SM. The GlycanBuilder and GlycoWorkbench glycoinforma@cs tools: updates and new developments. Biol Chem. 2012 Nov;393(11):1357-‐62. doi: 10.1515/hsz-‐2012-‐0135.

•  Ceroni A, Dell A, Haslam SM. The GlycanBuilder: a fast, intui@ve and flexible soDware tool for building and displaying glycan structures. Source Code Biol Med. 2007 Aug 7;2:3. PubMed PMID: 17683623; PubMed Central PMCID: PMC1994674.

March 26, 2014 65

Acknowledgements

Johns Hopkins: Shuang Yang and Punit Shah

NIH/NHLBI Programs of Excellence in Glycosciences (PEG):

Jerry Hart, Natasha Zachara, Jenny Van Eyk, Hui Zhang, Subroto Chatterjee, Kevin Yarema, Alan Bush

etc.)

Thank You

[email protected]

March 26, 2014 67

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