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本帖最后由细胞海洋于 2010-6-28 11:09 编辑 $ c' y* n" D4 b* ^  b1 T
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Proteomics in Practice
A Guide to Successful Experimental Design) s7 }8 b3 H+ ~0 ?* U7 a5 B

Abbreviations, Symbols, Units XV
Introduction 1
1 History 1
2 Critical Points 83 r5 A$ Y% N1 `- X9 U0 W
2.1 Challenges of the Protein Samples 8
2.1 Challenges of the Analysis Systems 11
3 Proteomics Strategies 12
3.1 Proteome Mapping 125 `" w6 B# P7 Q+ g. X
3.2 Differential Analysis 12
3.3 Time Point Experiments 13
3.4 Verification of Targets or Biomarkers 132 j2 q+ e. _" f1 Z9 s- W/ v- r
3.5 Integration of Results into Biological Context 13: x* w( \& [  H! V, |
3.6 Systems Biology 13
4 Concept of Experimental Planning 147 \9 V0 P0 K! L$ G
4.1 Biological Replicates 14
4.2 Pooling of Samples: Yes or No? 14
4.3 Pre-fractionation of Samples: Yes or No? 14' C9 ^. r( h1 U) K' F+ Z3 h# r
4.4 Which is the Best Workflow to Start With? 15/ }) W9 G- M( ?$ [8 y
Part I: Proteomics Technology
1 Electrophoretic Techniques 19& f, G, i3 f# |( s& P: m  h
1.1 The Principle of Electrophoresis and Some Methodological
Background 19
1.1.1 Free Flow Electrophoretic Methods 20' S5 @% \- O1 d" a
1.1.2 Gels for Electrophoretic Techniques 211 }/ e. _/ A# B
1.1.3 Electroendosmosis Effects 21
1.2 Polyacrylamide Gel Electrophoresis 22

1.2.1 The Polyacrylamide Gel 22% P2 {2 ~3 e- A9 ~& k( [" \( ^' T
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
1.4.2 Preparation of IEF Gels 44. e$ E2 b2 d0 z: J! x- F
1.4.3 Isoelectric Focusing in Proteomics 452 y7 K; W8 Q  m# f+ z( u
1.5 Two-dimensional Electrophoresis 535 d. t6 {( H' L' ^
1.5.1 Sample Preparation 53
1.5.2 Pre-labeling of Proteins for Difference Gel Electrophoresis 687 _9 H; \% {  M+ @$ n2 M$ z* r
1.5.3 First Dimension: Isoelectric Focusing in IPG Strips 77: \; ]3 l4 e0 M1 f4 y
1.5.4 Second Dimension: SDS Electrophoresis 1008 T0 _+ r. h+ @
1.5.5 Detection of Protein Spots 119
1.6 Image Analysis 125& W" j, j$ i  i& `+ s) S
1.6.1 Image Acquisition 1251 g/ P( X; m, D3 \0 f
1.6.2 Image Analysis and Evaluation 129
1.6.3 Use of 2-D Electrophoresis Data 1373 X  R. B" Y( f6 u, i2 x7 N
1.7 Spot Handling 1370 V, |  D& C' E. [# a
1.7.1 Spot Picking 1397 Q2 G) m% _6 v+ v
1.7.2 Protein Cleavage 141
Liquid Chromatography Techniques 151+ _( x3 b) [2 V0 Y" o  c
2.1 Basic Principles of Important Liquid Chromatography
Techniques 151
2.1.1 Ion Exchange Chromatography 153, p5 r* p3 ~/ X1 P- H1 x. L
2.1.2 Reversed Phase Chromatography 162, M$ }3 X, o3 P% G* W+ Q1 H
2.1.3 Affinity Chromatography 167
2.1.4 Gel Filtration 172! K4 D  ~  F( ~3 l: u3 K& l
2.2 Strategic Approach and General Applicability 174
2.3 Liquid Chromatography Techniques and Applications in Proteome/ ^, E; J  d: p) X
Analysis 1762 a; v/ x& O7 ]) [: B& s8 @
2.3.1 Peptide Separation 1763 O5 b" K+ G8 G" r8 a5 x
2.3.2 2DLC Peptide Separation 179
2.3.3 Affinity Chromatography and LC-MS/MS 187$ u3 u% U9 u1 z) F& Z* Q1 U
2.3.4 Protein Pre-fractionation 189
2.4 Practical Considerations and Application of LC-based Protein
Pre-fractionation 1949 z" a- N8 v5 A5 A5 c2 B3 C1 z
2.4.1 Sample Extraction and Preparation 196
2.4.2 Experimental Setup 197
2.4.3 Ion Exchange Chromatography and
Protein Pre-fractionation 198
Contents
2.4.4 Reversed Phase Chromatography and& P9 I2 R8 s, J, k# y0 p/ [  C' n/ }
Protein Pre-fractionation 205
2.4.5 Fraction Size and Number of Fractions 210* A+ u, @" R7 k( X% i& z
2.5 Critical Review and Outlook 211
3 Mass Spectrometry 215
3.1 Ionization 218( Q7 U1 g. T0 v& `8 Y9 x% D$ L
3.1.1 Matrix Assisted Laser Desorption Ionization 2180 j7 i, A0 C% |+ c8 C" b
3.1.2 Electrospray Ionization 222: l/ S  S/ F" b$ S0 B
3.2 Ion Separation 225% [' [3 M6 O8 t- g) \* ?
3.2.1 Time-of-Flight Analyzer 225
3.2.2 Triple Quadrupole Analyzer 227
3.2.3 Quadrupole Ion Trap 228
3.2.4 Quadrupole Time-of-Flight 2307 W3 Q$ C+ x. G# e! m0 [
3.2.5 Hybrid Triple Quadrupole Linear Ion Trap 231
3.2.6 TOF/TOF Analyzer 231% G' {: s- Y/ i1 L
3.2.7 Fourier Transform Ion Cyclotron 232, [+ D9 q' d1 K: {, w9 C+ f* y: P
3.2.8 Orbitrap 233
3.3 Generating MS Data for Protein Identification 233
3.3.1 Peptide Mass Fingerprint 234
3.3.2 Peptide Mass Fingerprint Combined With Composition. M: T0 V+ k1 r, A, z" d
Information 237( n- _& J/ J; K; k! B) S
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence6 Q3 X1 U- e2 g5 W4 C
Information 238
3.3.4 Tandem Mass Spectrometry 242
3.4 Protein Characterization 258- \3 {! }' X$ P
3.4.1 Phosphorylation Analysis 2595 v3 J: D  _( O, T8 @: ~4 S
3.4.2 Affinity Chromatography 260* A- w, {$ D$ f+ S/ _- c
3.4.3 Chemical Derivatization 261; w. T! Z/ u$ \4 k7 U9 |5 O
3.4.4 Glycosylation 263
3.5 Protein Quantification Using Mass Spectrometry 264! y8 {+ U; ]4 o' u# e! C% R
3.5.1 Stable Isotope Labeling Approaches 2649 V; q% u( e# `4 t
3.5.2 Isotope-coded Affinity Tags 2652 }. |* n* l" j) m. o8 S+ |3 _( J! s
3.5.3 Stable Isotope Labeling with Amino Acids in Cell Culture 266
3.5.4 AQUA 267+ R% C. w; ]+ `2 D1 D
3.5.5 iTRAQ 267
3.5.6 Non-labeling Software Approaches 268) }3 G) P1 n  X/ ?% v
3.6 MS Strategies 2712 z, e* t" k; Z& M2 g
3.6.1 Bottom up Approach 271
3.6.2 Top down Approach 2727 }) O5 g, ?7 K0 ^7 O% [
4 Functional Proteomics: Studies of Protein–Protein Interactions 273+ ?; \2 D) t% z) l3 x
4.1 Non-immunological Methods 273, ~1 q5 [* b! \4 a( M+ H
4.1.1 Separation of Intact Multi-protein Complexes 273
4.1.2 Probing with Interaction Partners 2739 U8 [: R  k' h
4.1.3 Surface Plasmon Resonance 274
4.2 Antibody-based Techniques 275) V) `* s" _4 n7 ]& @
4.2.1 Western Blotting and Dot Blots 275
4.2.2 Protein Microarrays 276! O% F. `+ a$ J+ L$ |* {. E+ o
Part II: Practical Manual of Proteome Analysis 279
Equipment, Consumables, Reagents 281
Step 1: Sample Preparation 2873 `/ }, ^$ \. L. U" f) X6 i+ d$ a
Step 2: Fluorescence Difference Gel Electrophoresis 299
Step 3: Isoelectric Focusing 309
Step 4: SDS Polyacrylamide Gel Electrophoresis 323
Step 5: Scanning of Gels Containing Pre-labeled Proteins 357
Step 6: Staining of Gels 361" J" D7 `+ U; [
Step 7: Image Analysis and Evaluation of DIGE Gels 373& I9 t, [3 y4 Z
Step 8: Spot Excision 383
Step 9: Sample Destaining 387
Step 10: Protein Digestion 389
Step 11: Microscale Desalting and Concentrating of Sample 393; X. C( N9 Q6 d5 k, r
Step 12: Chemical Derivatization of the Peptide Digest 397# d8 ]/ Y/ e/ p
Step 13: MS Analysis 399- V" H" B3 F7 _! T  m* Q
Step 14: Calibration of MALDI-ToF MS 403* j0 h) Y9 F' V$ ]7 Q7 k1 m
Step 15: Preparing for a Database Search 407
Part III: Trouble Shooting 4115 M, m6 ~" r! |4 q, \" L
1 Two-dimensional Electrophoresis 4134 A/ Q$ J& f: Q; Z
1.1 Sample Preparation 413- ~8 [: `# x1 D
1.2 Isoelectric focusing in IGPG strips 414% \' `# K, A& G0 i
1.3 SDS PAGE 416) A/ ~) j2 J3 N5 \8 D/ k0 U
1.4 Staining 417
1.5 DIGE Fluorescence Labeling 418, Q0 P) P4 ?: V+ f1 V% A2 F! H
1.6 Results in 2-D Electrophoresis 421  \2 ^7 O  p$ U+ Q, o
2 Mass Spectrometry 429
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