PDF电子书：蛋白质组学最新版Introduction to Proteomics [Liebler[1].Humana.2002] - 经典PDF电子书下载区干细胞之家



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Proteomics in Practice* m9 B2 T/ y! O2 Y! v( u  a1 x
A Guide to Successful Experimental Design
6 O) W- X/ j0 O; c* z% w
Abbreviations, Symbols, Units XV
Introduction 1
1 History 13 a! q3 b) j. m
2 Critical Points 8+ g2 i! }1 d. h/ {1 o& n7 |) Q
2.1 Challenges of the Protein Samples 8
2.1 Challenges of the Analysis Systems 11' ?! v' ?: j: I3 O/ a
3 Proteomics Strategies 12
3.1 Proteome Mapping 12; x* P7 w: N, N5 ?2 W! m1 {- g
3.2 Differential Analysis 127 ?# ~& n( E$ ]
3.3 Time Point Experiments 137 X- K$ z# C( P1 A3 u
3.4 Verification of Targets or Biomarkers 13- z: i6 a. F: ^5 [; w" B6 B
3.5 Integration of Results into Biological Context 13
3.6 Systems Biology 13
4 Concept of Experimental Planning 143 F* |" E/ m# U4 }! |- H3 T
4.1 Biological Replicates 14
4.2 Pooling of Samples: Yes or No? 14
4.3 Pre-fractionation of Samples: Yes or No? 14
4.4 Which is the Best Workflow to Start With? 15- D4 I$ s" q. ]1 X( d
Part I: Proteomics Technology' y% Y0 `: p% v! q5 g# c! z0 L
1 Electrophoretic Techniques 19
1.1 The Principle of Electrophoresis and Some Methodological- j5 Q$ Y6 d$ ~" k' C/ b; K9 q9 ^1 O3 c
Background 191 J6 O) @2 Q; T" B1 F% q
1.1.1 Free Flow Electrophoretic Methods 20
1.1.2 Gels for Electrophoretic Techniques 21
1.1.3 Electroendosmosis Effects 21
1.2 Polyacrylamide Gel Electrophoresis 229 [1 g7 A' g8 G. T$ C9 F- |
; r( T/ N9 i" B+ }2 W
1.2.1 The Polyacrylamide Gel 22
1.2.2 SDS Polyacrylamide Gel Electrophoresis 27
1.2.3 Blue Native Electrophoresis 32
1.2.4 Cationic Detergent Electrophoresis 34
1.3 Blotting 35
1.3.1 Electrophoretic Transfer 36
1.3.2 Protein Detection on the Membrane 36
1.4 Isoelectric Focusing 38
1.4.1 Theoretical Background 39) w  p0 a8 u$ S' f
1.4.2 Preparation of IEF Gels 44
1.4.3 Isoelectric Focusing in Proteomics 45+ f+ z7 J# P2 w" _
1.5 Two-dimensional Electrophoresis 53
1.5.1 Sample Preparation 537 S/ i3 D; F3 k( w7 w+ J
1.5.2 Pre-labeling of Proteins for Difference Gel Electrophoresis 68
1.5.3 First Dimension: Isoelectric Focusing in IPG Strips 77
1.5.4 Second Dimension: SDS Electrophoresis 100) M4 @& @' l7 v
1.5.5 Detection of Protein Spots 1196 E: V# M8 N  w" T  \/ j( g+ v! z
1.6 Image Analysis 125
1.6.1 Image Acquisition 125$ m# T+ I4 v' y3 q
1.6.2 Image Analysis and Evaluation 1291 T. I# N, x' W6 y" |
1.6.3 Use of 2-D Electrophoresis Data 137& B6 U  P4 S( l( l( I
1.7 Spot Handling 137' p' e# i" {6 H- z
1.7.1 Spot Picking 139
1.7.2 Protein Cleavage 141
Liquid Chromatography Techniques 151% R& d3 {8 H3 A) ?" U4 J4 K- A
2.1 Basic Principles of Important Liquid Chromatography
Techniques 151
2.1.1 Ion Exchange Chromatography 153% k6 [: z/ C& o$ a6 g
2.1.2 Reversed Phase Chromatography 162
2.1.3 Affinity Chromatography 167
2.1.4 Gel Filtration 172
2.2 Strategic Approach and General Applicability 174% e) _. x! k9 \
2.3 Liquid Chromatography Techniques and Applications in Proteome
Analysis 176
2.3.1 Peptide Separation 176
2.3.2 2DLC Peptide Separation 179
2.3.3 Affinity Chromatography and LC-MS/MS 187% M/ f! T( f  @1 L& c) G
2.3.4 Protein Pre-fractionation 189
2.4 Practical Considerations and Application of LC-based Protein* ~' C9 m1 B# h3 x& ]+ [( g0 K
Pre-fractionation 1946 U) d6 |; u( A0 W" r: E) L; u
2.4.1 Sample Extraction and Preparation 196
2.4.2 Experimental Setup 197% v' Y& g# S; [& U% U- P& g# l6 j
2.4.3 Ion Exchange Chromatography and8 d; \: a# u5 H' d5 Y' l$ \- K2 B
Protein Pre-fractionation 198. x" c3 w; A8 h: O2 y5 P
Contents; i; B  v- R7 @9 P# \9 u7 [# s2 u
2.4.4 Reversed Phase Chromatography and7 `8 V! N4 @# Q! x0 Z5 K
Protein Pre-fractionation 2057 k5 F2 s5 Z0 G$ r0 g3 i6 ^2 s
2.4.5 Fraction Size and Number of Fractions 210- L9 W1 ^  Y% L6 [4 o+ Z( K
2.5 Critical Review and Outlook 211
3 Mass Spectrometry 215
3.1 Ionization 218( C! P5 R7 Z6 Y: u+ T- U
3.1.1 Matrix Assisted Laser Desorption Ionization 2186 H! m4 a3 ]1 Y8 b/ y( d
3.1.2 Electrospray Ionization 222, C) g; r/ O+ T+ M  ]: G
3.2 Ion Separation 225# C4 [) w: s- P2 f8 Q/ I, I
3.2.1 Time-of-Flight Analyzer 225
3.2.2 Triple Quadrupole Analyzer 227
3.2.3 Quadrupole Ion Trap 228. Y- C, I: \) V2 k7 U  S* U
3.2.4 Quadrupole Time-of-Flight 230
3.2.5 Hybrid Triple Quadrupole Linear Ion Trap 231
3.2.6 TOF/TOF Analyzer 231
3.2.7 Fourier Transform Ion Cyclotron 2324 X5 I8 t  m' M
3.2.8 Orbitrap 233! x( b* J: A* w% R
3.3 Generating MS Data for Protein Identification 233! ?+ l7 }! n# T( Z, U
3.3.1 Peptide Mass Fingerprint 234$ C3 [+ a& S4 |! }
3.3.2 Peptide Mass Fingerprint Combined With Composition9 j6 e' Q, ^8 ?! ?& X1 x0 l
Information 237
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence
Information 238
3.3.4 Tandem Mass Spectrometry 2424 G6 j: G+ ^0 R2 g3 S8 \) w" I
3.4 Protein Characterization 258
3.4.1 Phosphorylation Analysis 259
3.4.2 Affinity Chromatography 260/ O- I9 L* M: ~& d& p% L! Q2 {8 i7 [
3.4.3 Chemical Derivatization 261
3.4.4 Glycosylation 263' d$ O' R- q' e1 @" P$ c+ Z
3.5 Protein Quantification Using Mass Spectrometry 264
3.5.1 Stable Isotope Labeling Approaches 264
3.5.2 Isotope-coded Affinity Tags 265. O  M1 _+ l; i" X7 b- G% u& j
3.5.3 Stable Isotope Labeling with Amino Acids in Cell Culture 266) x( [2 ]5 W5 U
3.5.4 AQUA 267
3.5.5 iTRAQ 267- ~) a. w0 R$ b. \
3.5.6 Non-labeling Software Approaches 268
3.6 MS Strategies 271& c. X' F7 P1 ^! u8 y
3.6.1 Bottom up Approach 271
3.6.2 Top down Approach 272& ^# s* U' b! p- j3 c
4 Functional Proteomics: Studies of Protein–Protein Interactions 273, u$ v' V/ {9 ]+ s" X" Z9 h. l" X
4.1 Non-immunological Methods 2734 B0 n: ~4 r# X  x
4.1.1 Separation of Intact Multi-protein Complexes 273
4.1.2 Probing with Interaction Partners 273- K  n5 u$ ]$ g! h8 M
4.1.3 Surface Plasmon Resonance 2743 A# L, W$ G% O% \; C+ w1 N$ O9 R
4.2 Antibody-based Techniques 2758 w9 z& x2 W/ s# p/ M8 g+ p
4.2.1 Western Blotting and Dot Blots 2757 b: {+ c( u8 v+ x5 v: V8 `
4.2.2 Protein Microarrays 276
Part II: Practical Manual of Proteome Analysis 279, q. r3 C! m( L" Q5 x" d
Equipment, Consumables, Reagents 281
Step 1: Sample Preparation 2873 W8 t  \8 Y8 v7 ~8 {
Step 2: Fluorescence Difference Gel Electrophoresis 299
Step 3: Isoelectric Focusing 309
Step 4: SDS Polyacrylamide Gel Electrophoresis 3238 G  |0 {! W3 [  u1 K" v' y- X# K
Step 5: Scanning of Gels Containing Pre-labeled Proteins 357
Step 6: Staining of Gels 361
Step 7: Image Analysis and Evaluation of DIGE Gels 373
Step 8: Spot Excision 3835 P7 H1 f5 x+ v' B7 d8 I
Step 9: Sample Destaining 387; @. A, `. x* i, G% N# F1 Y
Step 10: Protein Digestion 389
Step 11: Microscale Desalting and Concentrating of Sample 393
Step 12: Chemical Derivatization of the Peptide Digest 397
Step 13: MS Analysis 399
Step 14: Calibration of MALDI-ToF MS 403/ F$ @9 ?' _4 e; {3 b) Y* P
Step 15: Preparing for a Database Search 407
Part III: Trouble Shooting 411% h$ y5 |% ]7 F& N5 T) y
1 Two-dimensional Electrophoresis 4137 ~( D8 o1 F& O
1.1 Sample Preparation 413
1.2 Isoelectric focusing in IGPG strips 414/ S! |2 v- [" c* B. w, Q  B, O2 i
1.3 SDS PAGE 416
1.4 Staining 4175 s9 z9 b4 s' D/ K
1.5 DIGE Fluorescence Labeling 4183 f& ^5 w2 i7 B7 B2 j% g- `9 w
1.6 Results in 2-D Electrophoresis 421; g# p5 z& B- p" B# I6 e  [
2 Mass Spectrometry 429% @5 ^  o' w6 G

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