Linear Growth of Glycomics

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1 2/7/17 Glycomics & Glycoproteomics Lance Wells, omplex arbohydrate Research enter, Department of Biochemistry & Molecular Biology, and hemistry University of Georgia NIGMS Biomedical Glycomics Linear Growth of Glycomics 16 Glycomics/Proteomics KeyWord in PUBMED Publications 13: Glycomics is 4.5% of Proteomics PUBMED Papers 1 Normalized to 3 3: Glycomics is 1.% of Proteomics PUBMED Papers Year 1

2 2/7/17 Glycomics in the Spotlight (literature) Athens Guidelines for the Publication of Glycomic Studies Block diagram of a Mass Spectrometer Block diagram of a Tandem Mass Spectrometer All MS do one thing: Measure 2

3 2/7/17 Quan%ta%ve Strategies LABELING STRATEGY PROTEOMIS GLYOMIS Label free Spectra count TIM/Prevalence In vitro 18O H 2O labeling SILA In vivo (Stable Isotope Labeling with Amino acids in ell culture) In MS2 TMT 13 H 3I or D3I Permethyla%on QUIBL IDAWG??? N- and O- glycan structures determined by Total- ion monitoring Or L- MS- Quan;ﬁca;on By peak intensity (normalized to standards)) 3

4 Relative quantification between 2 samples of released and permethylated N-glycans via isotope labeling with light/heavy iodomethane * * * +1 Da 4

5 /7/17 Light Medium Heavy Medium Amide- 14 N L-glutamine Gln-14 Amide- 15 N L-glutamine GLN reverse phase PNGase F digestion N-linked Glycan Mixture 18 reverse phase Permethylation Permethylated Glycans Harvest & ombine Mixed Protein Powder Peptide Mixture Mass Spectrometry Homogenization and delipidation Tryptic digestion β-elimination O-linked Glycan Mixture Deionization Permethylation Permethylated Glycans Relative Abundance Light Heavy Gln-14 GLN-15 Quantification by Full MS Relative Abundance haracterization by MS/MS Figure 5 A. [M+Na] + : and (mono) : * * * * Relative Abundance hde = 1.74 hes

6 Figure 5 B. [M+Na] + : and (mono) hde =.23 hes Relative Abundance : * * * Table 3: Relative quantification of O-glycan expression levels in hess and hde using IDAWG (Ratio=hDE/hESs) (Prevalence > 1%) Structure Prevalence Ratio V % 1.11.% % % % % % %!! hde! "! and % % % % % % and % % hes! #! $! % % % % % % 6

7 /7/17 Pulse-hase experiment designed for dynamic IDAWG Heavy Media X 4 Light X 4 X 3 Light Light X 2 omplete Media Media Media hr 12 hr 24 hr 36 hr Labeling X 1 Harvest X 1 X 1 X 1 X 1 Release N- and O-linked glycans Permethylation hr-- >95% Heavy Relative Abundance

8 6hr Relative Abundance hr Relative Abundance

9 24hr Relative Abundance hr Relative Abundance

10 5% degradation time and proportion of remodeling at 5% degradation time for 9 major O-glycans Structure 5% degradation time (hours) Proportion of remodeling at 5% degradation time (%) Rep1 Rep2 Rep1 Rep Glycomics by MS -Generating data very robust -Data Analysis is getting better -Quantitative technologies have been developed

11 2/7/17 Glycan site mapping: Glycoproteomics Lance Wells, omplex arbohydrate Research enter, Department of Biochemistry & Molecular Biology, and hemistry University of Georgia NRR Biomedical Glycomics 11

Site Mapping and haracterization M P Q N G S W E K A F S Y D P R S T P G L I T I H A N G R E S S M K Q N V S L PNGase F Treatment and N-linked Glycosylation Site-mapping Secreted Proteins from

12 Site Mapping and haracterization M P Q N G S W E K A F S Y D P R S T P G L I T I H A N G R E S S M K Q N V S L PNGase F Treatment and N-linked Glycosylation Site-mapping Secreted Proteins from Adipocytes (insulin responsive vs insulin resistant) Sulfated glycoprotein 1 precursor (SGP-1) gi (K)TVVTEAGNLLKDN#ATQEEILHYLEK (K)FSELIVNN#ATEELLVK (K)LVLYLEHNLEKN#STKEEILAALEK Follistatin-related protein 1 precursor gi (K)GSN#YSEILDK Haptoglobin gi (K)VVLHPN#HSVVDIGLIK (K)NLFLN#HSETASAK (K)VVHYEN#STVPEKK N-X-S/T lipoprotein lipase gi (R)TPEDTAEDTHLIPGLADSVSNHFN#HSSK vimentin gi 781 (R)QVQSLTEVDALKGTN#ESLER Adipsin gi (K)LSQN#ASLGPHVRPLPLQYEDK Decorin gi (R)ISDTN#ITAIPQGLPTSLTEVHLDGNK Hemopexin gi (R)SWSTVGN#TAALR 56 proteins with 83 N-linked sites (all N-X-S/T) 12

13 N-linked Site Mapping from ona-enriched glycopeptides from Drosophila heads--272 sites mapped from 197 Proteins Pileup of the 272 N-linked Sites to Determine onsensus beyond N-X-S/T Asn 1 T / s NQ NQ ST ST DE DE H * H KR KR AG AG Y Y F F W * W ILV ILV P P * M * M Asn 1 T / s Absolute Requirement Not Allowed Down > 2-fold STD (p<.5) Up > 2-fold STD (p<.5) * occurrence less than 3% Down > 3-fold STD (p<.1) oncerns: PNGaseF/A, Deamidation, -terminal O-18 ell. May 28;141(5): Precision mapping of an in vivo N- glycoproteome reveals rigid topological and sequence constraints. Zielinska DF, Gnad F, Wiśniewski JR, Mann M. >6, Sites Mapped from Mouse Organs >99% of Sites Match N-X-S/T(), X is not Pro, ~1% of sites used ys in place of S/T Small percentage of sites (<1%) were N-X-V or NG (Real of False-Positives???) 13

14 O-Glycopeptides GalNAc Man Fuc Glc Gal Xyl GlcNAc Ser/Thr Ser/Thr Ser/Thr Ser/Thr Hyl Ser Hyp β Ser/Thr No PNGaseF equivalent for O-Glycans O-Glycanse has very restricted specificity N H O H H 2 Glycan O β-elimination OH - N H H 2 O Michael Addition DTT DTT H H 2 N H O BEMAD --an enrich glycopept 14

Differential isotopic tagging of both cysteine and post-translationally modified ser/thr through β-elimination/michael addition with light (d) and heavy (d6) DTT.

15 Differential isotopic tagging of both cysteine and post-translationally modified ser/thr through β-elimination/michael addition with light (d) and heavy (d6) DTT. O N H S IH 2 H H 2 O Alkylated ysteine N H NH 2 (GlcNAc or phosphate) O H H 2 O O-Glycan or O-phosphate Modified Serine (or threonine) β-elimination β-elimination N H H 2 O Dehydroalanine (or Michael Addition Light DTT (d) or Heavy DTT (d6) OH OH HSH 2 HHH 2 SH HSd 2 ddd 2 SH OH OH N H DTT (d or d6) H H 2 O oncerns: Specificity, efficiency, recovery Quantifying Peptides with D- and D6-DTT Theoretical: 1 to 1 ; Experimental 1 to.98, 1 fmol scale 15

16 Ammonia-Based β-elimination (ABBE) Replace NaOH with NH 4 OH NH 3 also acts as a nucleophile OH ( Da) =.984 Da (1+) NH 2 ( Da) Rademaker et al, 1998, Anal Biochem, 257: Teo_BPPK2_Std #1-7 RT: AV: 19 NL: 8.6E7 T: FTMS + p NSI Full ms [15.-.] Full MS of BPP P S V P V S G S A P G R [M+2H] 2+ =

17 Teo_BPPK2_ABBE1 #3323 RT: AV: 1 NL: 2.2E8 T: FTMS + p NSI Full ms [3.-.] Full MS of BPP ABBE P S V P V S NH2 G S A P G R [M+3H] 3+ = A. O! S! IH 2!! NH 2! B. N! H! H! H 2!!! O! Alkylated ysteine! β Elimination" N! H! H 2!!! Michael Addition! Light DTT (d) or Heavy DTT (d6)! N! H! H! DTT (d or d6)! H 2!!! N! H! H! (Glycan)! O! H 2!!! β Elimination" O! Dehydroalanine! (or! OH HSH 2 HHH 2 SH! OH OH HSd 2 ddd 2 SH! OH O! O! O-Glycan Modified Serine (or threonine)! 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 (d) 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. 17

18 Site Mapping and haracterization -Where we want to be! M P Q N G S W E K A F S Y D P R S T P G L I T I H A N G R E S S M K Q N V S L (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 18

19 Alpha-Dystroglycan Figure 2. Released O-Man and O-GalNAc linked glycans 19

Identification of Glycans using TIM-MS Pseudo Neutral Loss Activated Data Dependant MS 3 for Glycopeptide Mapping MS Survey Scan MS survey scan MS survey scan MS

20 Identification of Glycans using TIM-MS Pseudo Neutral Loss Activated Data Dependant MS 3 for Glycopeptide Mapping MS Survey Scan MS survey scan MS survey scan MS survey scan MS/MS scan Neutral loss? Yes Yes Top N peaks? No No Yes SEQUEST ID MS/MS/MS scan If we have purified protein and glycomics data

21 Figure 3. Fragmentation of O-GalNAc α-dg glycopeptide 21

22 22

Assignment of Glycan Structure by Residue

the phosphorylated trisaccharide structure to a

23 Assignment of Glycan Structure by Residue Assignment of Modified Glycopeptide 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 327:88 23

24 Another O- Glycan site mapping solu;on High ollision Dissocia.on (HD) 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-ID-ETD-HD #5157 RT: AV: 1 NL: 4.53E6 T: FTMS + c NSI d Full ms @hcd35. [ ] HexNAc , HexNAc , HexNAc- 6 +1, HexNAc +1, 4.9 b2- H2O, HexNAc- H2O +1, b3- H2O, b3, y3, y9- HexNAc +2, y- HexNAc +2, y5, y6, MH- HexNAc +2, S+HexNAc Δ29.12 MH +2, y7- HexNAc, y8- HexNAc, b7, y9- HHexNAc, y7, y- HexNAc, y9, 3.51 y11- HexNAc, HD spectra y7 GlcNAc PSVPV S GSAPGR y6 MH- HexNAc,11.58 y, y11, MH,

9 8 D b2, 154.548 1.85 8 HD (zoomed in) GlcNAc PGGSTPVSSANMM 7 6 5 Relative Abundance 4 3 122.

64 [ 8 H O 3 N] + 172.74 1 179.2 4 186.75 [ 8 H 12 O 4 N] + 4.84 HexNAc +1 [ 8 H 14 O 5 N] + 239.

23E6 T: ITMS + c NSI d sa Full ms2 657.34@etd. [5.-1325.

58 65 6 55 5 45 4 35 3 25 15 y2, 232.33 y8 +3, 312.5 z4, 385.51 z5, 472.66 z6, 529.

25 9 8 D b2, HD (zoomed in) GlcNAc PGGSTPVSSANMM Relative Abundance [ 6 H 8 O 2 N] [ 7 H 8 O 2 N] [ 6 H O 3 N] [ 8 H O 3 N] [ 8 H 12 O 4 N] HexNAc +1 [ 8 H 14 O 5 N] BSA-OGlcNAcpepmix-2nmol-ID-ETD-HD #585 RT: 44.9 AV: 1 NL: 2.23E6 T: ITMS + c NSI d sa Full ms @etd. [ ] z7 GlcNAc PSVPV S GSAPGR z6 MH +2, ETD spectra MH, y2, y8 +3, z4, z5, z6, S+HexNAc Δ29.1 z7- HexNAc, b6, z7, z8, c11- HexNAc, y9, 3.77 z- H2O, z, c11, z11, 1.57 y11, MH- H2O,

26 Promising Approaches: ED/ETD Fragmentation gbpp_recal #17-65 RT: AV: 49 NL: 3.11E5 T: FTMS + p ESI Full ms2 657.@. [ 18.-.] x Z Z5 Z ppm GlcNAc PSVPVSGSAPGR Z7 Z8 x15 Z Z11 ED Fragmentation of O-GlcNAc Modified Peptide. Fragments in BLUE contain O-GlcNAc-Ser. Z Simultaneous O-Man and O-GalNAc Analysis by ETD MS/MS Live etdsup_ #1 RT:. AV: 1 NL: 1.8E4 T: ITMS + p NSI sa Full ms2 6.3@etd13. [17.-.] , , Relative Abundance Z * Ac-IRT*T*T^S^GVPR-NH 2 * Man ^ GalNAc Z9 9 (Z) Z Z Z5^ * Z6^ 5^ Z7* ^ Z8* () 26

27 A. B. Pseudo'Neutral'Loss'Acvated'Data' Dependent'MS 3 'for'o:man'pepde'mapping ' HD$triggered+ETD+Analysis+for+ O$Man+Pep:de+Mapping + MS Survey Scan MS Survey Scan MS survey scan MS survey scan MS survey scan MS/MS scan MS survey scan MS survey scan MS survey scan MS/MS scan w/ HD Neutral loss? No Oxonium Ion? No Yes Yes Top N peaks? No Yes Yes Top N peaks? No Yes SEQUEST ID Yes SEQUEST ID MS/MS/MS scan ETD Scan 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, 3, 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<) to complete fragment off the glycan and then achieve good peptide fragmentation for identification. B. HD-triggered ETD takes advantage of scanning out glycopeptide fragments in the Orbitrap rapidly to look for the generation of glycan oxonium ions (163, 4, 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. Take Home Points 1. Enzymatic approaches for N-linked site mapping 2. Beta-elimination chemical approaches for O-linked site mapping 3. Glycopeptide analysis requires glycomics and proteomics to confine the search space and for structural determination 4. MSn approaches work for direct glycopeptide analysis 5. ExD (ETD, ED, etc.) look promising for glycopeptides 6. HD-triggered ETD approaches for mining deep and can aid identification 27

LC-nSI/MS/MS---Protein Identification

LC-nSI/MS/MS---Protein Identification 2Mar31M #2184 RT: 3.9 AV: 1 L: 2.97E6 T: + c d Full ms2 41.47@36. [ 13.-19.] 1 9 9 8 8 7 7 6 6 4 4 3 3 2 2 1 42.2 32. 13.6 6.2 66.2 389.2 46.2 18.2 631.1 371. 613. 22.1 719. 763. 631.7 919.2 2 3 4 6 7