Linear Growth of Glycomicsglycobiology/GlycomicGlyco... · 2017. 2. 7. · 2/7/17 7 Pulse-Chase...
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2/7/17 1 Lance Wells, Complex Carbohydrate Research Center, Department of Biochemistry & Molecular Biology, and Chemistry University of Georgia [email protected] Glycomics & Glycoproteomics NIGMS Biomedical Glycomics Linear Growth of Glycomics Glycomics/Proteomics KeyWord in PUBMED Publications 2003: Glycomics is 1.0% of Proteomics PUBMED Papers 2013: Glycomics is 4.5% of Proteomics PUBMED Papers 0 200 400 600 800 1000 1200 1400 1600 2002 2004 2006 2008 2010 2012 2014 Normalized to 2003 Year
Transcript of Linear Growth of Glycomicsglycobiology/GlycomicGlyco... · 2017. 2. 7. · 2/7/17 7 Pulse-Chase...
2/7/17
1
Lance Wells, Complex Carbohydrate Research Center, Department of Biochemistry & Molecular Biology, and Chemistry
University of Georgia [email protected]
Glycomics & Glycoproteomics
NIGMS Biomedical Glycomics
Linear Growth of Glycomics
Glycomics/ProteomicsKeyWord in PUBMED
Publications
2003: Glycomics is1.0% of ProteomicsPUBMED Papers
2013: Glycomics is4.5% of Proteomics
PUBMED Papers 0
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600
800
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1200
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2002 2004 2006 2008 2010 2012 2014
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Glycomics in the Spotlight (literature)
2013 2013
Athens Guidelines for the Publication of Glycomic Studies
All MS do one thing: Measure m/z
Block diagram of a Tandem Mass Spectrometer
Block diagram of a Mass Spectrometer
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Quan%ta%ve Strategies
LABELING
STRATEGY PROTEOMICS GLYCOMICS
Label‐free Spectra count TIM/Prevalence
In‐vitro 18O‐H2O labeling
13C‐CH3I or CD3I
Permethyla%on
QUIBL
In‐vivo SILAC
(Stable Isotope Labeling with
Amino acids in Cell culture)
In MS2 TMT ???
IDAWG
N-‐ and O-‐glycan structures determined by “Total-‐ion monitoring” Or LC-‐MS-‐Quan;fica;on
By peak intensity (normalized to standards))
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Relative quantification between 2 samplesof released and permethylated N-glycans
via isotope labeling with light/heavy iodomethane
+1 Da
* * *
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Amide-15N L-glutamine “GLN-15”
Amide-14N L-glutamine“Gln-14”
Light Medium Heavy Medium
Harvest & Combine
Mixed Protein PowderHomogenization and delipidation
Peptide Mixture
O-linked Glycan MixtureN-linked Glycan Mixture
Tryptic digestion
C18 reverse phasePNGase F digestion β-elimination
Permethylated Glycans Permethylated Glycans
C18 reverse phasePermethylation
DeionizationPermethylation
Characterization by MS/MSQuantification by Full MS
Mass Spectrometry
300 400 500 600 700 800 900 1000 1100 1200m/z
05
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40
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5055
60
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Rel
ativ
e A
bund
ance
486.23
901.93
799.88 966.47
474.23998.51
300 400 500 600 700 800 900 1000 1100 1200m/z
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486.23
901.93
799.88 966.47
474.23998.51
1030 1031 1032 1033 1034 1035 1036m/z
05
101520
2530354045505560657075
808590
95100
Rel
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e Ab
unda
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1030 1031 1032 1033 1034 1035 1036m/z
05
101520
2530354045505560657075
808590
95100
Rel
ativ
e Ab
unda
nce
HeavyGLN-15
LightGln-14
1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 0
10
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m/z
Rel
ativ
e Abu
ndan
ce
1705.858
1708.859
1706.862
1709.847
1707.865
1710.849
1711.852
Figure 5 A. [M+Na]+: 1705.862 and 1706.854 m/z (mono)
hEShDE = 1.74
:* *
**
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1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 0
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m/z
Rel
ativ
e Abu
ndan
ce1432.736
1435.729
1433.738
1436.729
1434.739
1437.7331438.736
Figure 5 B. [M+Na]+: 1432.741 and 1435.735 m/z (mono)
: *
**
hEShDE = 0.23
Structure m/z Prevalence Ratio CV
983.52 21.78% 1.11 20.20%
1256.64 20.22% 1.09 14.42%
1344.69 17.60% 2.64 30.21%
895.46 8.20% 0.87 13.56%
and 534.29 6.76% 1.04 17.20%
1793.91 5.81% 0.64 61.95%
1705.86 4.93% 2.54 29.48%
and 1432.74 4.70% 0.41 37.70%
1879.95 2.12% 1.75 49.39%
1157.60 1.99% 0.99 29.78%
779.42 1.03% 0.79 26.42%
Table 3: Relative quantification of O-glycan expression levels in hESCs and hDE using IDAWG(Ratio=hDE/hESCs) (Prevalence > 1%)
!! "!
#! $!
hDE!
hES!
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Pulse-Chase experiment designed for dynamic IDAWG
X 1Complete
Labeling
X 1
X 4 X 4 X 3 X 20 hr 12 hr 24 hr 36 hr
X 1 X 1 X 1Harvest
Release N- and O-linked glycans
Permethylation
IDAWG-hES-PC-12hr-14N-O-trapping-072009 #34 RT: 2.59 AV: 1 NL: 7.59E6T: FTMS + p NSI Full ms2 [email protected] [1225.00-1275.00]
1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265m/z
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Rel
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e A
bund
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1259.62
1257.63
1258.631260.621256.63
1261.63
1259.111258.11 1262.631260.111255.56 1263.631260.78 1264.601257.11
Heavy Media LightMedia
LightMedia
LightMedia
1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 0 5
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m/z
Rel
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ce
1259.622
1260.626
1258.626
1261.628
1262.632
0hr-- >95% Heavy
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1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 0 5
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Rel
ativ
e Abu
ndan
ce
1256.635
1259.626
1257.633
1260.629
1258.631
1261.632
1262.635
6hr
1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 0 5
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m/z
Rel
ativ
e Abu
ndan
ce
1256.630
1259.622
1257.629
1260.6251258.629
1261.627
1262.628
12hr
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1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 0 5
10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95
100
m/z
Rel
ativ
e Abu
ndan
ce1256.630
1259.621
1257.631
1260.624
1258.631
1261.6271262.633
24hr
1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 0 5
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100
m/z
Rel
ativ
e Abu
ndan
ce
1256.629
1259.622
1257.630
1260.623
1258.631
1261.6261262.626
36hr
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Structure50% degradation time
（hours）Proportion of remodeling at 50%
degradation time (%)
Rep1 Rep2 Rep1 Rep218.6 19.4 1.6 1.120.7 22.6 0.0 0.07.7 8.4 0.0 0.0
16.2 15.6 9.0 9.7
14.9 14.1 26.8 25.420.4 18.1 16.9 21.218.4 19.8 9.3 8.421.3 25.3 21.5 16.922.1 19.4 27.9 27.0
50% degradation time and proportion of remodeling at 50% degradation time for 9 major O-glycans
Glycomics by MS
-Generating data very robust
-Data Analysis is getting better
-Quantitative technologies have been developed
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Lance Wells, Complex Carbohydrate Research Center, Department of Biochemistry & Molecular Biology, and Chemistry
University of Georgia
Glycan site mapping: Glycoproteomics
NCRR Biomedical Glycomics
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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
PNGase F Treatment and N-linked Glycosylation Site-mapping
Secreted Proteins from Adipocytes (insulin responsive vs insulin resistant)
N-X-S/T
56 proteins with 83 N-linked sites (all N-X-S/T)
Sulfated glycoprotein 1 precursor (SGP-1) gi|3914939 (K)TVVTEAGNLLKDN#ATQEEILHYLEK (K)FSELIVNN#ATEELLVK (K)LVLYLEHNLEKN#STKEEILAALEK
Follistatin-related protein 1 precursor gi|2498391 (K)GSN#YSEILDK
Haptoglobin gi|8850219 (K)VVLHPN#HSVVDIGLIK (K)NLFLN#HSETASAK (K)CVVHYEN#STVPEKK Decorin gi|6681143 (R)ISDTN#ITAIPQGLPTSLTEVHLDGNK
Adipsin gi|673431 (K)LSQN#ASLGPHVRPLPLQYEDK
Hemopexin gi|1881768 (R)SWSTVGN#CTAALR
lipoprotein lipase gi|12832783 (R)TPEDTAEDTCHLIPGLADSVSNCHFN#HSSK
vimentin gi|2078001 (R)QVQSLTCEVDALKGTN#ESLER
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-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 Asn 1 T / s 3 4 5 6 7 8 9 10NQ 0.157 0.152 0.099 0.045 0.202 0.246 0.509 -0.339 -0.413 -1.076 3.427 0.197 -9.000 0.246 0.040 -0.076 0.094 0.197 -0.076 0.152 0.045 NQST 0.110 -0.151 -0.061 0.024 -0.247 0.019 -0.410 -0.203 0.247 0.138 -9.000 0.019 2.977 -1.410 0.590 0.138 -0.066 -0.156 -0.066 0.180 0.253 STDE -0.638 0.052 0.052 -0.081 -0.081 0.129 -0.233 -0.041 -0.456 -0.340 -9.000 0.089 -9.000 -0.134 0.004 0.419 0.089 -0.041 0.129 -0.280 0.052 DEH * 0.448 0.443 -1.364 -0.779 0.443 0.630 0.800 0.215 -0.785 -0.370 -9.000 -9.000 -9.000 -1.370 -0.785 -0.785 -0.048 -0.370 -0.048 -0.779 0.636 HKR 0.063 0.013 0.058 0.143 0.101 0.095 -0.038 0.680 0.256 0.095 -9.000 -0.533 -9.000 0.008 -0.992 -0.407 -0.185 0.217 0.400 0.183 0.406 KRAG -0.111 -0.473 -0.361 0.093 0.093 -0.167 0.200 0.126 0.126 0.370 -9.000 0.433 -9.000 0.551 0.008 0.088 -0.167 0.126 -0.729 -0.258 -0.162 AGY -0.050 -0.318 0.061 0.061 -0.318 0.262 0.355 -0.645 0.442 0.525 -9.000 -0.323 -9.000 -0.838 0.162 -0.475 -0.186 -0.475 0.442 -0.055 0.360 YF -0.763 0.125 0.232 0.672 0.009 0.004 -0.581 -0.122 0.419 0.667 -9.000 0.326 -9.000 0.119 -0.411 -0.581 -0.411 -0.996 0.119 -0.406 -0.991 FW * 1.211 -0.116 0.469 0.206 -0.116 -0.122 -0.537 0.463 -0.537 0.200 -9.000 0.200 -9.000 -0.122 -1.122 -1.122 0.200 0.200 0.200 -2.116 -0.531 WILV 0.067 0.181 0.012 -0.123 0.087 -0.101 0.106 -0.046 0.057 0.032 -9.000 0.130 -9.000 0.286 0.130 0.176 -0.020 0.153 -0.101 0.111 -0.438 ILVP 0.453 -0.055 0.267 -0.318 -0.318 -0.475 -0.838 -0.838 -1.323 -0.645 -9.000 -9.000 -9.000 -0.186 -0.060 -0.186 0.603 -0.060 0.162 0.267 0.061 PC * -0.181 -0.509 -0.187 -0.509 0.299 -2.514 -0.192 0.071 -1.514 -0.514 -9.000 0.486 -9.000 -0.514 0.071 -0.929 0.808 -0.514 0.071 0.076 -0.187 CM * -0.774 0.636 0.221 -1.364 -1.364 -0.048 -0.785 -0.785 0.630 -1.370 -9.000 -0.048 -9.000 0.438 -0.785 0.215 -0.370 -0.785 -0.370 0.221 -0.042 M
-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 Asn 1 T / s 3 4 5 6 7 8 9 10
Absolute Requirement Not Allowed Down > 2-fold STD (p<.05)
Up > 2-fold STD (p<.05) * occurrence less than 3% Down > 3-fold STD (p<.01)
N-linked Site Mapping from ConA-enriched glycopeptides from Drosophila heads--272 sites mapped from 197 Proteins
Pileup of the 272 N-linked Sites to Determine Consensus beyond N-X-S/T
Concerns: PNGaseF/A, Deamidation, C-terminal O-18
Cell. 2010 May 28;141(5):897-907.Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints.Zielinska DF, Gnad F, Wiśniewski JR, Mann M.
>6,000 Sites Mapped from Mouse Organs
>99% of Sites Match N-X-S/T(C), X is not Pro, ~1% of sites used Cys in place of S/T
Small percentage of sites (<1%) were N-X-V or NG (Real of False-Positives???)
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O-Glycopeptides
Ser/Thr
GalNAc
Ser/Thr
Man
Ser/Thr
Fuc
Ser/Thr
GlcNAc
Ser/Thr
Glc
Hyl HypSer
Gal Xyl
β
No PNGaseF equivalent for O-Glycans
O-Glycanse has very restricted specificity
β-Elimination CNH
C
O
CH2
DTTCNH
C
O
CH2
OGlycan
H CNH
C
O
CH2H
DTT
Michael Addition
OH-
BEMAD --Can enrich glycopeptides before --Can map via the dehydro-amino acid --Can enrich the peptides after
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β-Elimination
CNH
C
O
CH2
Alkylated Cysteine
Dehydroalanine(or
CNH
C
O
CH2
SICH2
H
CNH
C
O
CH2H
DTT (d0 or d6)
HSCH2CHCHCH2SH
Michael Addition
C
O
NH2
OH
OH
HSCd2CdCdCd2SH
OH
OH
Light DTT (d0) or Heavy DTT (d6)
Differential isotopic tagging of both cysteine and post-translationally modified ser/thr through β-elimination/Michael addition with light (d0) and heavy (d6) DTT.
O-Glycan or O-phosphateModified Serine (or threonine)
CNH
C
O
CH2H
O
(GlcNAc or phosphate)
β-Elimination
Concerns: Specificity, efficiency, recovery
Quantifying Peptides with D0- and D6-DTTTheoretical: 1 to 1 ; Experimental 1 to 0.98, 1 fmol scale
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Ammonia-Based β-Elimination (ABBE) � Replace NaOH with NH4OH
� NH3 also acts as a nucleophile
Rademaker et al, 1998, Anal Biochem, 257: 149-160.
OH ( 17.0027 Da)
NH2 (16.0187 Da)
0.984 Da (1+) =
Teo_BPPCK2_Std #1-107 RT: 0.01-1.09 AV: 19 NL: 8.60E7T: FTMS + p NSI Full ms [150.00-2000.00]
554.0 554.5 555.0 555.5 556.0 556.5 557.0 557.5m/z
0
5
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15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rela
tive
Abun
danc
e
555.8013
556.3014
556.8024
557.3038
P S V P V S G S A P G R [M+2H]2+= 555.7990
Full MS of BPP
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Teo_BPPCK2_ABBE1 #3323 RT: 51.22 AV: 1 NL: 2.02E8T: FTMS + p NSI Full ms [300.00-2000.00]
370.0 370.2 370.4 370.6 370.8 371.0 371.2 371.4 371.6 371.8m/z
0
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Rela
tive
Abun
danc
e
370.5416
370.8745
371.2083
371.5427
P S V P V SNH2 G S A P G R [M+3H]3+= 370.5406
Full MS of BPPABBE
B.
A.
Figure 2: Site mapping N- and O-glycoslyation sites on proteins. A. Strategy for site-mapping N-glycosylation sites relies on PNGaseF release of glycans converting the previously modified Asn residue to and Asp residue (mass shift of 1 dalton). If 18O-water is used the mass shift is 3 daltons. This allows for comparsion between two samples where one uses 16O- and the other 18O-water. B. Strategy for site-mapping O-glycoslyation site relies on beta-elimination coupled with Michael addition with DTT. DTT is available isotopically heavy (d6) so two samples cam be compared using light (d0) and heavy (d6) DTT respectively. The protein amount can also be quantified accurately in the same experiment based on the cysteine-containing peptides that are subject to elimination and addition as well.
β�Elimination"
C!N!H!
C!
O!
CH2!
Alkylated Cysteine!
Dehydroalanine!(or !
C!N!H!
C!
O!
CH2!
S!ICH2!
H!
C!N!H!
C!
O!
CH2!H!
DTT (d0 or d6)!
HSCH2CHCHCH2SH!
Michael Addition!
C!
O!
NH2!
OH
OH
HSCd2CdCdCd2SH!
OH
OH
Light DTT (d0) or Heavy DTT (d6)!
O-Glycan Modified Serine (or threonine)!
C!N!H!
C!
O!
CH2!H!
O!
(Glycan)!
β�Elimination"
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Site Mapping and Characterization -Where we want to be!
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%)
What do we need for direct glycopeptide analysis?
1. Usually need enrichment
2. Need glycomics/proteomics of enriched material
3. Ideally would like to have sites of glycosylation
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Alpha-Dystroglycan
Figure 2. Released O-Man and O-GalNAc linked glycans
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Identification of Glycans using TIM-MS
MS Survey Scan
MS survey scan MS survey scan
MS survey scan MS/MS scan
Neutral loss? No
Yes Top N peaks? No
Yes
MS/MS/MS scan
SEQUEST ID
Yes
Pseudo Neutral Loss Activated Data Dependant MS3 for Glycopeptide Mapping
http://www.thermo.com If we have purified protein and glycomics data
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Figure 3. Fragmentation of O-GalNAc α-DG glycopeptide
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Assignment of Glycan Structure by Residue
Assignment of the phosphorylated trisaccharide structure to a specific glycopeptide of alpha-dystroglycan using MSn approaches. Displayed is a MS3 spectra demonstrating the presence of the phoshotrisaccharide . Science 2010 327:88
Assignment of Modified Glycopeptide
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Another O-‐Glycan site mapping solu;on
High Collision Dissocia.on (HCD) Fragmenta.on Genera.ng oxonium ions
Electron Transfer Dissocia.on (ETD) Fragmenta.on Targe.ng Modified pep.des
Pep.de Sequencing and Modifica.on Site Mapping
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
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
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
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204.084HexNAc+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 250m/z
0
10
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30
40
50
60
70
80
90
100R
elat
ive
Abu
ndan
ce
BSA-OGlcNAcpepmix-2nmol-CID-ETD-HCD #5085 RT: 44.09 AV: 1 NL: 2.23E6T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1325.00]
100 200 300 400 500 600 700 800 900 1000 1100 1200 1300m/z
0
5
10
15
20
25
30
35
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80
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90
95
100
Re
lativ
e A
bu
nd
an
ce
MH, 1314.58
MH-‐H 2O,1297.53
z11, 1200.57
c11, 1155.37
z10-‐H 2O, 1094.79
y9, 1030.77
z8, 918.54
z7, 819.61
b6, 769.57
MH+
2 , 657.51
z7-‐HexNAc
, 616.57
z6, 529.60
z5, 472.66
z4, 385.51
y8+3, 312.50
y2, 232.33
S+HexNAc Δ290.01m/z
c11-‐He
xNAc
, 952.43
y11, 1216.62
z10, 1113.58
PSVPV S GSAPGR
z6
z7
GlcNAc
ETD spectra
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gbpp_Recal #17-65 RT: 0.17-1.04 AV: 49 NL: 3.11E5T: FTMS + p ESI Full ms2 [email protected] [ 180.00-2000.00]
300 400 500 600 700 800 900 1000 1100 1200 1300m/z
0
10
20
30
40
50
60
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100
Rel
ativ
e A
bund
ance
657.3386
1314.6809
328.6699 472.2516
529.2732
1271.6612
385.2195819.3852
616.3053 1094.5978917.44611156.5841
659.3430
972.49991255.6341911.4921
1030.5136
743.3290
x10 x15
GlcNAc
PSVPVSGSAPGR
+ 0.3 ppm
Z4
Z5
Z6 Z7
C7
Z8
Z10
Z11
Z12
ECD Fragmentation of O-GlcNAc Modified Peptide.Fragments in BLUE contain O-GlcNAc-Ser.
Promising Approaches: ECD/ETD Fragmentation
Simultaneous O-Man and O-GalNAc Analysis by ETD MS/MS
Live-120308-3-620etdsup_080312031606 #1 RT: 0.00 AV:1 NL: 1.08E4T: ITMS + p NSI sa Full ms2 [email protected] [170.00-2000.00]
400 600 800 1000 1200 1400 1600 1800m/z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e Ab
unda
nce
930.25
1817.58
908.67
1703.42
1844.50
1507.42354.08 592.25
844.50329.171159.42
1268.25 1450.42701.00 1532.17
411.00
828.171596.42
1005.17747.17 1090.33430.17 1344.33565.92
C2
C3*
C4*
C5^
C6^
C7
C9
(C10)
C10
Z3
Z4 Z5^ Z7*
Z6^
Z8*
Z9
Z10 (Z10)
C8
Ac-IRT*T*T^S^GVPR-NH2 * Man ^ GalNAc
+3, 620.6 m/z +1, 1857.9 m/z
2/7/17
27
MS Survey Scan
MS survey scan MS survey scan
MS survey scan MS/MS scan
Neutral loss? No
Yes Top N peaks? No
Yes
MS/MS/MS scan
SEQUEST ID
Yes
Pseudo'Neutral'Loss'Ac0vated'Data'Dependent'MS3'for'O:Man'Pep0de'Mapping'
MS Survey Scan
MS survey scan MS survey scan
MS survey scan MS/MS scan w/ HCD
Oxonium Ion? No
Yes Top N peaks? No
Yes
ETD Scan
SEQUEST ID
Yes
HCD$triggered+ETD+Analysis+for+O$Man+Pep:de+Mapping+
Figure 3: Two automated MS-based strategies for the detection of Glycopeptides. A. Pseudo-neutral loss MSn sequencing looks for a peptide fragment that has lost the weight of a sugar (162, 203, etc.) and if observed in the top N peaks (usually 3) triggers that peptide to be fragmented further in order to be able to sequence the peptide (shown is a MS3 strategy but the method can go MSn (n<10) to complete fragment off the glycan and then achieve good peptide fragmentation for identification . B. HCD-triggered ETD takes advantage of scanning out glycopeptide fragments in the Orbitrap rapidly to look for the generation of glycan oxonium ions (163, 204, etc.). If a glycan oxonium ion is observed in the top N peaks, the instrument slows down to isolate the parent peptide again and subject it to electron transfer dissociation (ETD) that allows for sequencing of glycopeptides without loss of the sugar residues. These two approaches are complementary and combined provide for a thorough characterization of glycopeptides directly from known glycoproteins with defined glycomic profiles.
A. B.
Take Home Points1. Enzymatic approaches for N-linked site mapping2. Beta-elimination chemical approaches for O-linked site
mapping3. Glycopeptide analysis requires glycomics and proteomics to
confine the search space and for structural determination4. MSn approaches work for direct glycopeptide analysis5. ExD (ETD, ECD, etc.) look promising for glycopeptides6. HCD-triggered ETD approaches for mining deep and can aid
identification
