Welcome to the world of. Room 6016, CLS

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1 Welcome to the world of mass spectrometrybased proteomics! Xiaolu Zhao, Ph.D. Room 6016, CLS Wuhan University

2 从 " 基因 " 到 " 蛋白 " 基因数 线虫 19,000 果蝇 13,500 拟南芥 27,000 人类 ~20,500

3 从 " 基因 " 到 " 蛋白 " 基因数 线虫 19,000 果蝇 13,500 拟南芥 27,000 人类 ~20,500 DNA RNA 基于质谱技术的蛋白质组学 - 全局性研究 蛋白质的表达水平蛋白质翻译后修饰蛋白质相互作用 PROTEIN ( 蛋白质 )

4 Protein and proteomics Mass spectrometry basics Mass spectrometry t for proteomics Quantitative proteomics Human Proteome and more

5 Protein and proteomics

6 Amino acid structure Side chain (R) H H N R C H C O OH Amino group Carboxyl group

7 Protein Backbone H R H R H R N C C OH N C C OH N C C OH H H O H H O H H O H 2 O H 2 O H R H H R R N C C N C C N C C OH H H O H O H O Amide bond

8 Amino Acid Residue H R H R H R N C C N C C N C C OH H H O H O H O H R N C C H O Amino acid residue structure

9 What is a proteome? The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism at a certain time. More specifically, it is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions.

10 What is Proteomics? Systematic (large scale) study of protein properties to obtain a global, integrated view of disease processes, cellular processes and networks at the protein level

11 What is Proteomics? Proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and, ultimately, their function. -Stan Fields in Science, 2001.

12 Every set of proteins of same modification can be called a proteome Phosphorylation Acetylation Ubiquitination Methylation GlcNAclation Phosphorylome Acetylome Ubiquitinome Methylome GlcNAclome

13 The tasks in proteomics Detection What and Where Quantification Compare dynamics

14

15 Technologies for Proteomics Adapted from Mallick and Kuster, Nature Biotechnology, 28: , 2010

16 Conceptual Organization of Proteomic Experiments Adapted from Mallick and Kuster, Nature Biotechnology, 28: , 2010

17 Challenges in proteomics

18 DNA: 4 bases Protein: 20 amino acids + PTM

19 DNA: similar biochemical property Protein: average size 450 aa wide range of solubility PTM degradation

20 The Human Plasma Proteome overwhelming dynamic range of at least 10 orders of magnitude

21 Proteomics - Challenges Sample Sampling Handling Complexity Reduction Chromatography Mass Spectrometry Bioinformatics Aebersold (2009) Nature Methods, 6, 411

22 Why yproteomics is a complement or alternative to mrna-based measurements? In areas in which microarray measurement is not feasible. Example: blood. The proteomic measurement already delivers the desired end point, namely the protein expression level of a gene of interest It is not limited to expression profiling of the whole cell. Cellular compartments and organelles and their time- resolved dynamics are readily accessible to this technology The large-scale measurement of protein modifications and their quantitative changes upon perturbations to the cell.

23 Figure: Quantitative Proteomics versus Transcriptomics (A) Overlap between the proteins identified in the example given in Figure 1 (blue) and the messages with present call (that is, significantly different from zero signal) in a quadruple microarray experiment of the normal HeLa cell proteome (green). (B) Label-free quantitation of about 4000 proteins identified in brain tissue samples from two separate individuals. Mass spectrometric intensity counts (added peptide signals) from the two separate runs are plotted against each other.

24 Mass spectrometry basics

25 Mass spectrometry to proteomics is like PCR to genomics

26 MS Principles Different elements can be uniquely identified by their mass

27 MS Principles Different compounds can be uniquely identified by their mass Butorphanol L-dopa Ethanol N -CH 2 - OH HO COOH -CH 2 CH-NH 2 CH 3 CH 2 OH HO HO MW = MW = MW = 46.1

28 What is Mass Spectrometry? Mass spectrometry is a powerful technique for chemical analysis that is used to identify unknown compounds, to quantify known compounds, and to elucidate molecular structure.

29 What does a mass spectrometer t do? 1. It measures mass better than any other technique. 2. It can give information about chemical structures. 3. It generate spectrum by separating gas phase ions of different mass to charge ratio (m/z) m=molecular or atomic mass z = electrostatic charge unit

30 Typical Mass Spectrum Relative e intens sity % Intensity Voyager Spec #1[BP = , 32728] Mass (m/z) m/z Characterized by sharp, 3.3E+ narrow peaks X-axis position: the m/z ratio of a given ion Height of peak: relative abundance of a given ion Peak intensity indicates the ion s ability to fly (some fly better than others)

31 Multiple Charging g Calculating mass-to-charge ratio (m/z) Consider a peptide with MW of With ESI-MS, charges by H + addition M + nh + MnH n+ Resultant ions formed are: When z = 1 m/z = ( )/1 = When z = 2 m/z = ( )/2 = 5001 When z = 3 m/z = ( )/3 = When z = 4 m/z = ( )/4 = 2501 When z = 5 m/z = ( )/5 = 2001

32 Figure from The Expanding Role of MS in Bio-technology G. Siuzdak

33 Stable isotopes of most abundant elements of peptides Element Mass Abundance H % C N O

34 Mass spectrum of peptide with 94 C-atoms (19 amino acid residues) Monoisotopic mass No 13 C atoms (all 12 C) One 13 C atom Two 13 C atoms

35 Monoisotopic mass Monoisotopic mass corresponds to lowest mass peak When the isotopes are clearly resolved the monoisotopic mass is used as it is the most accurate measurement.

36 Average mass Average mass corresponds to the centroid of the unresolved peak cluster When the isotopes are not resolved, the centroid of the envelope corresponds to the weighted average of all the the isotope peaks in the cluster, which h is the same as the average or chemical mass.

37 Mass Calculation (Glycine) NH 2 CH 2 COOH Amino acid R 1 NH CH 2 CO R 3 Residue Monoisotopic Mass 1 H = C = N = O = Glycine Amino Acid Mass 5xH + 2xC + 2xO + 1xN = amu Glycine Residue Mass 3xH + 2xC + 1xO + 1xN = amu

38 Amino Acid Residue Masses Monoisotopic Mass Glycine Aspartic acid Alanine Glutamine Serine Lysine Proline Glutamic acid Valine Methionine Threonine Histidine Cysteine Phenylalanine Isoleucine Arginine Leucine Tyrosine Asparagine Tryptophan

39 Amino Acid Residue Masses Average Mass Glycine Aspartic acid Alanine Glutamine Serine Lysine Proline Glutamic acid Valine Methionine Threonine Histidine Cysteine Phenylalanine Isoleucine Arginine Leucine Tyrosine Asparagine Tryptophan

40 Important performance factors Mass accuracy: How accurate is the mass measurement? Resolution: How well separated are the peaks from each other? Sensitivity: How small an amount can be analyzed?

41 Resolution 分辨率 : 分开两个邻近质量峰的能力, 高分辨率将目标物与复杂基质分离, 排除干扰, 确保质量精度 R m m m1 m2 未分开分辨率差 部分分开分辨率中等 全分开分辨率高

42 What if the resolution is not so good? Better resolution Poorer resolution Mass At lower resolution, the mass measured is the average mass.

43 Glossary:mass accuracy Mass accuracy: The absolute deviation between measured mass from true mass of an ion, typically expressed as an error value in ppm (parts per million). 1000±0.1 = 0.01% = 100 ppm

44 Mass measurement accuracy depends on resolution High resolution means better mass accuracy ppm error Resolution =18100 Counts ppm error Resolution = ppm error Resolution = Mass (m/z)

45 What do all MS instrument t have in common? Sample introduction Ionization Separate Count ions Collect results masses Minimize collisions, interferences

46 Sample Introduction High Vacuum System Inlet Ion Mass Data Source Analyzer Detector System HPLC GC Flow injection Sample plate

47 Ion Source High Vacuum System Inlet Ion Mass Data Source Analyzer Detector System MALDI ESI FAB LSIMS EI CI

48 Mass Spec Principles Sample + _ Ionizer Mass Analyzer Detector Find a way to charge an atom or molecule Place charged molecule in a magnetic field or subject it to an electric field and measure its speed or radius of curvature relative to its massto-charge ratio Detect ions using microchannel plate or photomultiplier tube

49 Nobel Prize in Chemistry 2002 "for the development of methods for identification and structure analyses of biological macromolecules" "for their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules" NMR John B. Fenn ESI b Koichi Tanaka MALDI b. 1959

50 Matrix-assisted laser desorption/ionization (MALDI) 基质辅助激光解析电离 Pulsed laser Sample plate Ions Extraction grid Absorption of UV radiation by chromophoric matrix and ionization of matrix Dissociation of matrix, phase change to super-compressed gas, charge transfer to analyte molecule Expansion of matrix at supersonic velocity, analyte trapped in expanding matrix plume (explosion/ popping ) popping Adopted from Nature, 422,200 (2003)

51 MALDI

52 MALDI 384 spots

53 Matrix for MALDI ToF 2,5-dihydroxybenzoic acid (DHB) α-cyano-4-hydroxy-cinnamic y y y acid 3,5-dimethoxy-4-hydroxycinnamic acid (sinapinic acid) Specific compounds for glycoprotein etc

54 Example of a MALDI-TOF Mass Spectrum Voyager Spec #1[BP = , 32728] E % Intensity Mass (m/z)

55 Electrospray Ionization (ESI) Atmosphere Vacuum Liquid id Spray chromatography needle Nozzle Sampling Nozzle Sampling cone Ions

56 质谱技术的核心 质量分析器 真空系统 进样系统 (LC 或者直大气压接进样 ) 离子化方式 质量分析器 检测器 数据处理系统 四级杆 (Q) 离子阱 / 线性离子阱 (IT/LTQ) 低分辨质谱 飞行时间 (TOF) 中高分辨质谱 傅立叶变换离子回旋共振 (FTICR) 静电场轨道阱 (Orbitrap) 超高分辨质谱

57 Analyzer Types What is the analyzer? Analyser is the section of instrument that separates ions of different m/z Many Different technologies: Magnetic Sector, Quadrupole, Ion Trap, ToF

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59 The quadrupole consists of four parallel metal rods Only ions of a certain m/q will reach the detector for a given ratio of voltages: other ions have unstable trajectories and will collide with the rods. This allows selection of a particular ion, or scanning by varying the voltages. Obtains a mass spectrum by sweeping across the entire mass range

60 MALDI-TOF Mass Spectrometry Bruker Autoflex Now available as Tof/ToF Easy to use walk up use after training. Highly automated Now can be used for imaging of Tissue samples

61 Q-TOF NANOSPRAY TIP MCP DETECTOR PUSHER ION SOURCE SKIMMER HEXAPOLE QUADRUPOLE HEXAPOLE COLLISION CELL HEXAPOLE TOF REFLECTRON

62 超高分辨质谱 傅立叶变换 FT FT-ICR 傅立叶变换离子回旋共振 Orbitrap 静电场轨道阱 B m / z k m / z 傅立叶变换质谱 当离子进入质量分析器后, 以和质荷比相关的特征频率作轨道方式运动, 随后离子被激发到其固有的轨道半径旋转, 由收集电极检测随时间变化的镜像电流 时域信号经 FT 变换器得到频率域信号, 继而转化为质谱图

63 独一无二的 Orbitrap 技术 中心电极 外纺锤电极 30 年来唯一基于全新理论的质量分 析器, 真空度比传统质量分析器高 3 个数量级以上, 稳定性极强

64 Orbitrap 逐渐成为质谱分析的金标准 Orbitrap 性能 9 年来飞速增长 ion (FWH HM) Mass s resolut Orbitrap Orbitrap Fusion Tof / QTof Orbitrap Elite QE HF QE LTQ Orbitrap Bendix Tof First Q-Tof Time progression (year)

65 性能卓越的 Q-Exactive 系列质谱仪 Q-Exactive (2011) 尖端四极杆 Q-Exactive Plus (2013) 超高场 Orbitrap Q-Exactive HF (2014) 四极杆 高灵敏度高选择性高动态范围 Orbitrap 高分辨率高质量精度

66 How do mass spectrometers get their names? Types of ion sources: Electrospray (ESI) Matrix Assisted Laser Desorption Ionization (MALDI) Types of mass analyzers: Quadrupole (Quad, Q) Ion Trap Time-of-Flight (TOF) Either source type can work with either analyzer type: MALDI-TOF, ESI-Quad... Analyzers can be combined to create hybrid instruments. ESI-QQQ, MALDI QQ TOF, Q Trap

67 Summary: acquiring a mass spectrum Ionization Mass Sorting (filtering) Detection Ion Ion Source Mass Analyzer Detector Form ions (charged molecules) Sort Ions by Mass (m/z) Detect ions Inlet Solid 25 Liquid 0 Vapor Mass Spectrum

68 Mass spectrometry for proteomics

69 Breaking Protein into Peptides Name Cleave Don't cleave N or C term Trypsin KR P CTERM Arg-C R P CTERM Asp-N BD NTERM Asp-N_ambic DE NTERM Chymotrypsin FYWL P CTERM CNBr M CTERM Formic_acid D CTERM Lys-C K P CTERM Lys-C/P K CTERM PepsinA FL CTERM Tryp-CNBr KRM P CTERM TrypChymo FYWLKR P CTERM Trypsin/P KR CTERM V8-DE BDEZ P CTERM V8-E EZ P CTERM CNBr+Trypsin M CTERM KR P CTERM

70 Protein ID: Two Main Approaches Peptide Mass Fingerprinting (PMF) Tandem Mass Spectrometry (MS/MS)

71 Peptide Mass Fingerprinting g (PMF)

72 Generalized Protein Identification by PMF Spot removed from gel Trypsin digest MS1 of tryptic peptides Library MATCH Artificial spectra built Artificially trypsinated Database of sequences (i.e. SwissProt)

73 Principles of Fingerprinting g Sequence Mass (M+H)( ) Tryptic Fragments >Protein 1 acedfhsakdfqea sdfpkivtmeeewe ndadnfekqwfe acedfhsak dfgeasdfpk ivtmeeewendadnfek d gwfe >Protein 2 acekdfhsadfqea sdfpkivtmeeewe nkdadnfeqwfe >Protein 3 acedfhsadfqeka sdfpkivtmeeewe ndakdnfeqwfe acek dfhsadfgeasdfpk ivtmeeewenk dadnfeqwfe acedfhsadfgek asdfpk ivtmeeewendak dnfegwfe

74 Principles of Fingerprinting g Sequence Mass (M+H)( ) Mass Spectrum >Protein 1 acedfhsakdfqea sdfpkivtmeeewe ndadnfekqwfe >Protein 2 acekdfhsadfqea sdfpkivtmeeewe nkdadnfeqwfe >Protein 3 acedfhsadfqeka sdfpkivtmeeewe ndakdnfeqwfe

75 Can We Do Better? Single Stage MS Tandem MS

76

77 Protein Identification Strategy I * Protein mixture Peptides Time (min) 1D, 2D, 3D peptide separation II 200 * Q1 Q2 Collision Cell Q m/z Tandem mass spectrum III Correlative sequence database searching m/z Theoretical Protein identification m/z Acquired

78 Cleavages Observed in MS/MS of Peptides low energy x n-i y n-i z n-i -HN--CH--CO--NH--CH--CO--NH- CO NH CO NH R i CH-R a i b i R c i

79 Fragmenting g a Peptide

80 MS/MS Peptide Fragmentation Ala-Gly-His-Leu-.Phe-Glu-Cys-Tyr b 1 y 1 b 2 y 2 b 3 y 3 b 4 y 4 b 5 y 5

81 Example of a ms/ms spectrum 100 YADSGEGDFLAEGGGVR 80 X lative Ab bundanc ce E A F D G E G S D Re m/z

82 Mascot MS/MS Form

83 Mascot MS/MS Output

84 Mascot MS/MS Output

85 MS/MS S vs PMF Advantages Provides precise sequence- specific data More informative than PMF methods (>90%) Can be used for de-novo sequencing (not entirely dependent d on databases) Can be used to ID post- trans. modifications Disadvantages Requires more handling, refinement and sample manipulation Requires more expensive and complicated equipment Requires high level expertise

86 Quantitative proteomics

87 Quantitative proteomics The goal of a quantitative proteomics analysis is to determine the changes in protein expression in a given cell from a given organism when subjected to a stimulus.

88 Label-free Quantitation Two examples of label-free quantitation: XIC extracted ion chromatogram SC spectral counting Avoid isotopes but instrumentation needs to be very reproducible

89 Label-free Quantitation - XIC if is identified by MS/MS as a peptide coming from protein X XIC of Find the peak area Only one peak because none of the other peptides have a molecular mass of Repeat the same process for all the other peaks B, C and D Sum all the peak areas in the XICs Concentration of protein X proportional to total area (need an internal standard)

90 Label-free Quantitation SC MS of each peaks MS of peak B Peak at is 3 rd highest so selected for MS/MS Count all the MS/MS spectra which came from a peptide which can be identified as coming from protein X (Spectral Count) Use e.g. protein Prospector to determine that t this peptide sequence is derived from protein X 90 Spectral count proportional to protein concentration (need internal standard)

91 Stable Isotope Labeling Strategies IN LABELING PROTEI Digest Metabolic stable isotope labeling li DATA COLLECTION Mass spectrometry DA ATA ANALY YSIS In ntensity In ntensity In ntensity m/z m/z m/z Aebersold and Mann, NATURE, 422, , 2003

92 SILAC stable isotope labelling of amino acids in cell culture Grow cells in media containing isotopically labelled amino acids O Typically e.g. N H 2 OH Lys4 alkly Dx4 subsitution ti +4 units Arg6 13 Cx6 subsitution +6 units Lys8-13 Cx Nx2 substitution +8 units Arg10-13 Cx Nx4 substitution +10 units H N NH 2 NH NH 2 O OH NH 2 Labelling arginine and lysine to ensure all tryptic peptides are labelled (Trypsin cuts at K or R)

93 SILAC stable isotope labelling of amino acids in cell culture L t t t i t Lyse, extract protein, separate trypsin digest, MS

94 SILAC mouse

95 SILAC SILAC mouse? Protein Chemical labeling

96 Stable Isotope Labeling Strategies IN LABELING PROTEI Isotope tagging by chemical reaction Label Digest Digest LECTION Digest Label Label DATA COL Mass spectrometry DA ATA ANALY YSIS In ntensity In ntensity In ntensity m/z m/z m/z Aebersold and Mann, NATURE, 422, , 2003

97 itraq Isobaric Tag for Relative and Absolute Quantification Reacts with NH 2 groups Adds tag of mass 145 to terminal NH2 groups and lysines NH N N O O H 3 C R MS/MS Fragmentation Rest of molecule + H 3 C N N CH + 2 Reporter ion 97

98 itraq 13 C x 3 15 N x 1 N N H 3C O Mw = 28 O O N O N 13 C x 2 N C 18 O O N O Produces an ion of Mw = 117 after fragmentation H 3 C N O O C H 3 13 C x 2 15 N x 1 N N O Produces an ion of Mw = 116 after fragmentation 13 CO O Mw = 30 O N O Mw = 29 Produces an ion of Mw = 115 after fragmentation etc 98

99 itraq

100 itraq This part gives the sequence information The low molecular weight region contains reporter ions Ratio tells us something about the relative abundance of this protein in the 4 samples 100

101 itraq reagent-8plex Protein Quantitation

102 Protein Dimethylation + 28 Da, light + 32 Da, intermediate + 36 Da, heavy Using formaldehyde globally label the N-terminus of peptide and ε-amino group of K through reductive amination.

103 SRM and Western Blots WB SRM Quality of the assay based on a single antibody depend on isotopically labeled reference peptides Quality of the results depends on the based quantification uses multiple intensity of a signals that are integrated into a band on the blot composite score indicating the protein quantity. limit of detection, linear dynamic range, ability to multiplex and reproducibility. For most of these characteristics MS- based methods now outperform Western blotting. Performance characteristic s

104 An example of SRM application A set of candidate biomarkers is verified by applying SRM assays for the candidate proteins to fractionated t sera from patient t and control groups, for example. Mutants of the target proteins can be monitored in the sampled population.

105 Human Proteome

106 2014

107 The adult/fetal tissues and haematopoietic cell types

108 Work flow

109 ~25million high-resolution tandem mass >2,000 LC-MS/MS runs using the MASCOT16 and SEQUEST17, Percolator18 293,000 non-redundant peptides (q value, 0.01 with a median mass measurement error ~260 parts per billion) The median number of peptides and corresponding tandem mass spectra identified per gene are 10 and 37, respectively the median protein sequence coverage was ~28%

110 Tissue-supervised hierarchical Tissue-supervised hierarchical clustering

111 Novel protein-coding regions in the human genome 16 million MS/MS spectra that did not match currently annotated proteins

112

113 Conclusion Proteomics is extremely valuable for understanding biological processes and advancing the field of systems biology. The ultimate goal of systems biology is the integration ti of data from these observations into models that might, eventually, represent and simulate the physiology of the cell.