Mass Spectrometry and Proteomics. Professor Xudong Yao Bioanalytical Chemistry Spring 2007

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1 Mass Spectrometry and Proteomics Professor Xudong Yao Bioanalytical Chemistry Spring 2007

2 Proteomics and -omics Roles of mass spectrometry Comparative proteomics Chemical proteomics

3 Protein, Proteome and Systems Biology Replication DNA RNA Protein Transcription Translation Genome Transcriptome Proteome Proteomics Analytical Definition of Proteomics Identity, Quantity and Function of All the Proteins in a Mixture Mass Spectrometry

4 Objectives of Proteomics Identity Quantity Time Proteome Function Interaction Activity Time-Dependence

5 Analytical Challenges in Post-genome Research Sample complexity Peak capacity Multi-dimensional separation Collective analysis Not traditional, one-by-one analysis Sensitive, specific and quantitative and the answers is Data treatment, analysis and achieving Hardware Software Researchers of multi-disciplinary training

6 m /z A Typical Proteomics Experiment 100 Sample Preparation Protein/Peptide Chemistry Enzymology Separations: Advanced HPLC and Electrophoresis % Mass Spectrometry New Ionization techniques Contemporary & New Mass Spectrometric Methods 0 Time Bioinformatics Applications of Mass Spectrometry and Database Searching Tools % % 0 Biology Protein Posttranslational Modification Protein Phosphorylation Proteolysis

7 Roles of Mass Spectrometry

8 The mass analysis process as compared to the dispersion of light by a prism Siuzdak, 2003

9 Mass Spectrometry Ion Source (ESI, MALDI) Mass Analyzer Vacuum Ion Detector Data System Sample Introduction Intensity Mass Spectrum m/z

10 Mass Analyzer Separate ions by mass/charge Common types Quadrupole mass filter (Q), Time-of-Flight (TOF), Ion Trap (IT), Fourier Transform Ion Cyclotron Resonance (FTICR) Tandem mass spectrometry Spatial, such as Q-q-TOF, TOF-TOF, Q-q-Q Temporal, such as IT, FTICR Spatial and Temporal, such as IT-FTICR, Q-q-FTICR, IT-TOF

11 Soft Ionizations of Biomolecules 1. Matrix-Assisted Laser Desorption/Ionization (MALDI) 2. Electrospray Ionization (ESI) Nobel Prize in 2002

12 Matrix-Assisted Laser Desorption/Ionization (MALDI) Generates Singly-Charged Ions Laser beam Sample probe + _ Matrix ion _ _ + + _ Analyte molecule Analyte ion Light-absorbing matrix MH +

13 Electrospray Ionization (ESI) Generates Multiply- Charged Ions

14 Tandem MS: Basic Concepts MS-1 Mass-selected precursor MS-2

15 Mass Spectrometry for Proteins and Peptides UNKNOWN PEPTIDE Structural elucidation Quantitative analysis Sensitive and automatic mixture analysis Sequencing proteins Identification of posttranslational modifications High-order structures and dynamics of proteins and protein dynamics Mass Spectrometer M +S ++A +++N ++++D +++++C H E M MSANDCHEM Protein/EST Database Protein Identification

16 Comparative Proteomics Gel or Non-gel Label or Non-label

17 Comparative Proteomics Relative Changes in proteins including concentration and composition Proteome 1 Proteome 2 Stable Isotope Coding Constant Ratio Separation Relative Quantitation Abnormal Ratios Sampling/Cell Culture Fractionation/Separation Mass Spectrometry Bioinformatics Identification of Proteins

18 Reduce sample complexity at the protein level: DDF (Differential Detergent Fractionation) T47D Cells Digitonin Supernatant Pellet Digitonin Extract Triton X-100 Supernatant Pellet 50K Triton X-100 Extract Tween/DOC Extract K 1. Tween/DOC Extraction (Nuclear Fraction) (Prolactin) 2. Tween/DOC Extraction (Nuclear Fraction) (Control) 3. Triton X-100 Extraction (Membrane/Organelle Fraction) (Prolactin) 4. Triton X-100 Extraction (Membrane/Organelle Fraction) (Control) 5. Digitonin Extraction (Cytosolic Fraction) (Prolactin) 6. Digitonin Extraction (Cytosolic Fraction) (Control) 7. Protein Ladder

19 GEL: 2-Dimensional Electrophoresis (2-DE) A Pandey; M Mann, Nat. Biotechnol Difficulties with: extreme pi proteins, low abundance, proteins, hydrophobic proteins Inefficient in-gel digestion of proteins for MS analysis Labor extensive

20 NON-GEL: MudPIT Analysis of Protein Complex Easier separation Easier automation Problematic proteins Small, large, hydrophobic, low abundance Easier sample preparation for MS analysis Computational capacity Quantitative capability Link et al. Nat. Biotechnol. 1999

21 A Glance at Proteomic Bioinformatics

22 Shotgun 2 Collision Induced Dissociation Mass Spectrometry 1 In-source Shotgun(CID) 2 In-collision-cell Shotgun(CID) 3 = * * Shotgun 2 (CID) In-Source CID of [M+3H] 3+ CID of [M+2H] 2+

23 Comparative Proteomics Relative Changes in proteins including concentration and composition Proteome 1 Proteome 2 Stable Isotope Coding Constant Ratio Separation Relative Quantitation Abnormal Ratios Sampling/Cell Culture Fractionation/Separation Mass Spectrometry Bioinformatics Identification of Proteins

24 Label: MS-Based Relative Quantitation Large differences in concentration Direct ESI/MALDI MS Small differences in protein concentration Stable isotope dilution: inherent choice Intensity m/z

25 Introduction of Stable Isotopes Criteria for isotope internal standards Ideally behaving the same before mass analysis Metabolic labeling during biosynthesis/bioprocess Post-biosynthesis/bioprocess labeling: chemical and enzymatic Functional groups on side chains: -SH, -OPO 3 H 3 Termini: N-terminal, C-terminal Active/Binding sites: Chemical Proteomics H 2 N (A 1 A 2 A 3 A n ) i COOH Coding Module

26 Advantages of Modular Design H 2 N (A 1 A 2 A 3 A n ) i Separation Module COOH Coding Module Isotope Coding Universal Important to small proteins Specific Efficient Minimal Structural Modification Chromatographic co-elution Stable during separation Separation Portable to all separation platforms, including affinity separation

27 Tryptic Incorporation of Two 18 O Atoms into Peptide C-Terminus H C O C H N E O + H * 2 O H C C * OH + H 2 N * R R

28 Adenovirus as Model System Minimal real system DNA + Proteins Known genome/proteome Predictable proteolytic peptides Defined architecture Predictable protein expression Comparative quantitation of Ad2/Ad5 proteins Dynamic range of 600-fold Shenk T. In Fundamental Virology, 1996 Capsid protein modeling membrane/hydrophobic proteins Mutations modeling post-translational modifications

29 3 Ad2 Virion 1 Ad5 Virion Lys-C H 2 18 O Trypsin H 2 16 O Combined Isotope-Coded Peptides Theoretical MW of Ad Tryptic Peptides MALDI-FTICR MS Most of peptides Ad2:Ad5 = 3:1 Protein Identification and Quantitation

30 MALDI-FTICR Mass Spectrum of Combined Digests Relative Intensity , Protein V TSTEVQTDPWFR 2 18 O 2 18 O , Protein VII TTVDDAIDAVVEEAR , Protein V VLRPGTTVVFTPGER 2 18 O

31 Controversies and Challenges in Proteolytic Labeling Reported controversies in tryptic 18 O labeling One 18 O incorporation for K-terminated peptides Low efficient incorporation of two 18 O for short peptides Two 18 O in each new peptides Capabilities of endoproteases for 18 O labeling Two 18 O incorporation by trypsin, Lys-C, and Glu-C only One 18 O incorporation by chymotrypsin Challenges for automated, large-scale application Amount and cost of H 2 18 O

32 Decoupling Proteolytic 18 O Labeling from Protein Digestion Proteins in solution prior to digestion Peptide labeling in small volume of H 2 18 O Separate optimization of digestion and labeling Automatic, high-throughput, large-scale applications

33 Dissection of Proteolytic Incorporation of Two 18 O Amide Bond Cleavage ½* O H C C R ½* OH + HO E H C R O C H N O + HO H C C H N. HO E R E H 2 *O H C R ½* O C ½* OH. HO E NH 2 H 2 *O H 2 *O H C * O C * OH + HO E H C H 2 O * O C * OH. HO E R R Carboxyl Oxygen Exchange Yao, Afonso, Fenselau. J. Proteom. Res. 2003, 2, 147.

34 Molecular Basis for Cleavage and Exchange Cleavage S 5 S 4 S 3 S 1 S 2 S 3 S 2 S 1 P 5 P 4 P 3 P P CONH 2 1 P 1 P 2 P 3 Native Peptide Substrate Exchange S 5 S 4 S 3 S 2 S 1 S 1 S 2 S 3 P 5 P 4 P 3 P 2 P 1 COOH Truncated Peptide Substrate Protease catalyzes exchange TWO 18 O INCORPORATION

35 16 O-to- 18 O Exchange Studied by MALDI-FTICR MS YGGFMR( 16 O 2 ) YGGFMR( 18 O 2 ) YGGFMR( 16 O 18 O) Relative Intensity m/z Time 0.5 min min

36 Determination of Reaction Initial Rates [ R] = [ R o ] I total ( I o Io, I2, I4, Mo, M2, M 4 )

37 Kinetics Comparison in R- and K-Peptides YGGFMR YGGFMK K cat (min -1 ) 3500± ±300 K M (µm) 1300± ±700 k cat /K M (µm -1 min -1 ) 2.6± ±0.14

38 Simultaneous Mass Spectrometric Determination of Kinetics for Trypsin-Catalyzed 16 O-to- 18 O Exchange Exchange Rate R R Complete Exchange for Mixture

39 Enzymatic 18 O Labeling Universal two 18 O labeling of proteolytic peptides by protease-catalyzed exchange Both K- and R-terminated peptides Chymotrypsin and pepsin for two 18 O labeling, in addition to trypsin, Lys-C, Glu-C, Both short and long peptides 4 Da mass increase at the C-terminus of proteolytic peptides to be differentiated in mass spectrometry

40 Mass Spectrometry of Peptide- 16 O 2 / 18 O 2 Pairs H 2 N (A 1 A 2 A 3 A n ) i Separation Module COOH Coding Module 18 O-labeling enabled mass spectrometric quantitation Effect of peak resolution on quantitation Analysis on different mass analyzer configurations More than relative quantitation from differential oxygen labeling

41 Relative Quantitation Using Paired Isotope Clusters Relative Intensity I 0 M I 4 I 2 Observed isotopic distribution of 1:1 mixture of 18 O and 16 O samples Theoretical natural isotopic distribution M M Mass/Charge Ratio = I I 4 o + 1 M M 2 o I I 2 o + M M 2 o 2 M M 2 o M M 4 o I I 5 1

42 Correlation of ESI Quantitation with Peptide UV Quantitation MS Ratio of [ 18 O]/[ 16 O] Peptide FVNQHLCGSHLVE slope: 0.94±0.03 r 2 : UV Ratio of [ 18 O]/[ 16 O] Reynolds, Yao, Fenselau. J. Proteom. Res. 2003, 1, 27.

43 BSA Peptide Sequence Labeling Consistency Sequence Position Unlabeled (I 0 ) Elution Time (minutes) a Labeled (I 4 ) Elution Time Ratio 1 b I 4 /I 0 (minutes) a ACFAVE KKFWGKYLYE TYVPKAFDE DKDVCKNYQE DKGACLLPKIE KQIKKQTALVE LLYYANKYNGVFQE YAVSVLLRLAKE AKDAFLGSFLYE DYLSLILNRLCVLHE Average Standard Deviation c Reynolds, Yao, Fenselau. J. Proteom. Res. 2003, 1, 27.

44 Correlation between MS and Western-Blot Quantification of Thioredoxin in Doxorubicin-Treated HeLa Cells SDS-PAGE Analysis of Whole Cell-Extracts: ESI-IT-MS Analysis of Anion-X Fraction 7: (Labeling: Dox Treated 16 O, Control 18 O) Mr Dox Control Dox Control data01_fraction7inverserepeat #1862 RT: AV: 1 SM: 15B NL: 3.42E6 T: + NSI d Z ms [ ] Dox 16 O 2 16 O 2 : 18 O 2 5:1 data01_fraction7inverserepeat #1863 RT: AV: 1 NL: 7.07E6 T: + c NSI d Full ms @35.00 [ ] XC= Relative Abundance Control 18 O 2 Relative Abundance kda Coomassie -Stain Western-Blot (Anti-Thioredoxin Ab) m/z Zoom Scan: Relative Quantification [M+2H] +2 =668.8 [M+2H + 18 O 2 ] +2 = MS 2 Scan: Identification m/z [M+H] + = K.TAFQEALDAAGDK.L Thioredoxin Courtesy of Dan Clark of Stratagene

45 Effect of Peak Resolution on 18 O/ 16 O Ratio (I) , Protein V TSTEVQTDPWFR 18O 2 18O , Protein VII TTVDDAIDAVVEEAR MALDI-FTICR , Protein V VLRPGTTVVFTPGER 18O 2 Protein II VII IX VIII Terminal % wt Relative Intensity 2.9± ± ± ± ±0.3 Yao, Freas, Ramirez, Demirev, Fenselau. Anal. Chem. 2001, 73, 2836.

46 Effect of Peak Resolution on 18 O/ 16 O Ratio (II) APC2_Human: 0.91 MALDI-TOF APC3_Human: 0.94 A1AH_Human: m/z m/z m/z APC2_Human: ESI-IT APC3_Human: A1AH_Human: m/z m/z m/z Heller, Mattou, Menzel, Yao. JASMS 2003, 14, 704.

47 Effect of Isolation Window Width on Quantitation Using 16 O/ 18 O y-ion Pairs on IT MS Isolation of I o = Isolation of I 4 = MH 2 2+ MH MS MS m/z m/z y 10 + y MS/MS MS/MS m/z m/z Heller, Mattou, Menzel, Yao. JASMS 2003, 14, 704.

48 Protein Sequence Ions Generated by Tandem Mass Spectrometry Mass Analyzer 1 Fragmenting the Selection Ion Mass Analyzer 2 x 4 y 4 z 4 x 3 y 3 z 3 x 2 y 2 z 2 x 1 y 1 z 1 H O H O H O H O H H H H H H 2 N C C N C C N C C N C C N C O C OH A 1 A 2 A 3 A 4 A 5 a 1 b 1 c 1 a 2 b 2 c 2 a 3 b 3 c 3 a 4 b 4 c 4

49 Masses of Amino Acid Residues

50 Quantitation Based on MS/MS Spectrum (y-ions) y 4 y 3 y 2 y 1 H O H O H O H O H H H H H H 2 N C C N C C N C C N C C N C O C OH MTVEPGLEPEVR A b 1 A 2 b 2 A 3 b 3 A 4 b 4 A 5 Relative Intensity O 2 18 O 2 Relative Intensity m/z m/z Yao, Freas, Ramirez, Demirev, Fenselau. Anal. Chem. 2001, 73, 2836.

51 16 O/ 18 O Paired Peptides Facilitate and Validate Peptide Sequencing IT MS/MS Relative Intensity C-terminal mass Da Q D A Y V S N-terminal mass Da QqTOF MS/MS m/z

52 Advantages of Modular Design H 2 N (A 1 A 2 A 3 A n ) i Separation Module COOH Coding Module Isotope Coding Universal Important to small proteins Specific Efficient Minimal Structural Modification Chromatographic co-elution Stable during separation Separation Portable to all separation platforms: LC/LC, solution IEF, affinity separation

53 Protein Pools of Digitonin Extract of MCF-7 Cells Cancer Cells Digitonin Extraction Digitonin fraction cytosolic soluble cytoskeletal proteins Supernatant 120,000xg 5,000xg Pellet Properties functional proteins soluble proteins Digitonin Extract C4 Fractionation Modified according to Ramsby, Makowski Method Mol. Biol., 112, 1999.

54 Rel. Int. Rel. Int. LC-MS of Peptides from MCF-7 Digitonin Fraction Base peak chromatography of total peptide mixture Time (min) TOF MS at 78 min Frequency Yao, Fenselau. ASMS Annual Conference, 2001 m/z MelR/WT Protein Ratio (MelR/WT) = 1.1 I 0 /I 4 Ratio (MelR/WT) = 1.1 ± % (184/223) peptides in 1.1 ± 0.3

55 Protein Expression Changes in MCF-7 Cells Upon Acquisition of Melphalan Resistance [Most Proteins in a Ratio (MelR/WT) of 1.1] (K)LLPQLTYLDGYDR(E) PHAPI2b /April protein pi = 4.0 MelR/WT = 2.0 (R)GIVTNWDDMEK(I) F1 NIH_MGC_88 Homo sapiens cdna clone MelR/WT = 2.6 Relative Intensity m/z Yao, Fenselau. ASMS Annual Conference, 2001

56 Analysis of Human Plasma Sample: Example 1 Human Plasma Abundance Protein Depletion Denaturing SEC Large Proteins Fraction X Small Proteins RP Tryptic Digestion 1x Peptide Pool 1 1x Peptide Pool 2 Enzymatic 16 O-Labeling 2x MG 16 O-Peptides Enzymatic 18 O-Labeling 1x MG 18 O-Peptides Combine Differentially-Labeled Peptides SCX MALDI-MS/MS µ-rp-hplc ESI-MS/MS Heller, Mattou, Menzel, Yao. JASMS 2003, 14, 704.

57 LC-MALDI & LC-ESI MS Analysis of Differentially 18 O/ 16 O-Labeled Peptides Present in Human Plasma LC-MALDI-MS (TOF) LC-nanoESI-MS (QTOF) LC-ESI-MS (IT) Rel. Int. m/z Heller, Mattou, Menzel, Yao. JASMS 2003, 14, 704.

58 Analysis of Human Plasma Sample: Example 2 Qian et. al., Smith MCP 2005, March 7

59 Coupling 16 O/ 18 O-Labeling and Solution Isoelectric Focusing for Peptide Analysis Comparative investigation of insoluble nuclear subproteome Sample separation after combining differentially-labeled peptides An, Fu, Gutierrez, Fenselau. J. Proteom. Res. 2005, 4, 2126.

60 Isotope-Coded Affinity Tag (ICAT) Unique Chemistry for -SH Affinity Tag Isotope-Coded Linker Gygi et al. Nat Biotechnol. 1999

61 Assembling Separation Module and Coding Module H 2 N (A 1 A 2 A 3 A n ) i Separation Module COOH Coding Module Protein H 2 18/16 O Glu-C 16/18 O 2 16/18 O 2 16/18 O 2 16/18 O 2 16/18 O 2 O I O NH O O NH O NH S NH FVNQHLCGSHLVE 16 O-16 O 2 O-18 O 2 O CH2 16/18 O 16/18 OH Relative Intensity Biotin Biotin S Mass/Charge

62 16 O/ 18 O-Labeling and Affinity Enrichment to Quantitate Proteins Liu, Qian, Strittmatter, Camp, Anderson, Thrall, Smith. Anal. Chem. 2004, 76, 5345.