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. H0 B4 Z. w! z9 k, W& V9 f
A Guide to Successful Experimental Design" L& y' @5 Z. C0 O7 N$ l

Abbreviations, Symbols, Units XV
Introduction 1
1 History 1
2 Critical Points 8
2.1 Challenges of the Protein Samples 8
2.1 Challenges of the Analysis Systems 11
3 Proteomics Strategies 127 s% z- a8 D" a* `
3.1 Proteome Mapping 12
3.2 Differential Analysis 12
3.3 Time Point Experiments 13; e. J$ M' `, x# F7 ?* g, o8 D8 m
3.4 Verification of Targets or Biomarkers 134 f# k1 s+ a: w* y- ?/ ?, z( b
3.5 Integration of Results into Biological Context 13
3.6 Systems Biology 133 l8 N+ m: v3 Q( y  R
4 Concept of Experimental Planning 145 m* Q' J3 ~3 O
4.1 Biological Replicates 14
4.2 Pooling of Samples: Yes or No? 149 q# v; ^5 O. y0 \  F
4.3 Pre-fractionation of Samples: Yes or No? 147 l8 G6 b0 W! c$ ^7 {- g' N
4.4 Which is the Best Workflow to Start With? 159 Q% i7 u6 Q$ i/ n% b
Part I: Proteomics Technology6 b+ Z. S! l4 @3 Z4 V
1 Electrophoretic Techniques 190 {9 S  {, W; T- K! X
1.1 The Principle of Electrophoresis and Some Methodological
Background 19" W% y0 A4 j2 w
1.1.1 Free Flow Electrophoretic Methods 20
1.1.2 Gels for Electrophoretic Techniques 21
1.1.3 Electroendosmosis Effects 21$ d6 x3 X$ [+ k* ^
1.2 Polyacrylamide Gel Electrophoresis 22
  f2 J7 C' y, i" F; [7 r
1.2.1 The Polyacrylamide Gel 22
1.2.2 SDS Polyacrylamide Gel Electrophoresis 27  V+ L( D1 @7 N. j3 ?5 l" R1 Z
1.2.3 Blue Native Electrophoresis 32
1.2.4 Cationic Detergent Electrophoresis 34
1.3 Blotting 35
1.3.1 Electrophoretic Transfer 368 a3 C, `8 O+ u" b/ l; }
1.3.2 Protein Detection on the Membrane 36  {! k$ T& h' e, U8 J
1.4 Isoelectric Focusing 38
1.4.1 Theoretical Background 39: @9 h4 Y2 F3 M7 `3 ~  x* O
1.4.2 Preparation of IEF Gels 44" Q- W, w. Y& L# s
1.4.3 Isoelectric Focusing in Proteomics 45  d/ j7 w: ]8 R+ U
1.5 Two-dimensional Electrophoresis 534 w0 [. }5 \2 j' h/ B% @
1.5.1 Sample Preparation 53, c. H* y5 a7 f$ L
1.5.2 Pre-labeling of Proteins for Difference Gel Electrophoresis 68- v- Q" R, G# O* T
1.5.3 First Dimension: Isoelectric Focusing in IPG Strips 77$ {' v4 h: _4 h/ S0 n  N! Z# W  `/ l
1.5.4 Second Dimension: SDS Electrophoresis 100
1.5.5 Detection of Protein Spots 1191 c5 t1 O* n" `2 }% i) F
1.6 Image Analysis 125
1.6.1 Image Acquisition 125
1.6.2 Image Analysis and Evaluation 129. ~1 l  T, y" _6 i0 V
1.6.3 Use of 2-D Electrophoresis Data 137
1.7 Spot Handling 137
1.7.1 Spot Picking 139
1.7.2 Protein Cleavage 141  I1 |' f) @: a; l
Liquid Chromatography Techniques 151
2.1 Basic Principles of Important Liquid Chromatography
Techniques 151# r: |- J$ B) d; i4 h3 y
2.1.1 Ion Exchange Chromatography 1535 Q6 ]5 `9 o( U# K
2.1.2 Reversed Phase Chromatography 162
2.1.3 Affinity Chromatography 167" _# E+ v- R) f, q) t. w  {" ]
2.1.4 Gel Filtration 172( s) t( q& z1 d, b; o
2.2 Strategic Approach and General Applicability 174
2.3 Liquid Chromatography Techniques and Applications in Proteome
Analysis 176
2.3.1 Peptide Separation 1763 Q7 d6 G# j+ {' h7 s( U5 D
2.3.2 2DLC Peptide Separation 179
2.3.3 Affinity Chromatography and LC-MS/MS 187, w/ t) h: U+ i
2.3.4 Protein Pre-fractionation 189) p. j' E# B& w5 w
2.4 Practical Considerations and Application of LC-based Protein* Q& T' {& O5 j# u
Pre-fractionation 194
2.4.1 Sample Extraction and Preparation 196
2.4.2 Experimental Setup 197* Q- V5 }/ t' v" @
2.4.3 Ion Exchange Chromatography and( W# i# L3 k5 n4 [
Protein Pre-fractionation 198/ L. c  o9 \8 g/ I: h
Contents5 I- L3 T3 I. @& }+ k6 Z, ]- v
2.4.4 Reversed Phase Chromatography and
Protein Pre-fractionation 2051 m) u" [- `5 M8 t
2.4.5 Fraction Size and Number of Fractions 210
2.5 Critical Review and Outlook 211
3 Mass Spectrometry 215" q) B$ P* ]! \5 ~, y) w
3.1 Ionization 218
3.1.1 Matrix Assisted Laser Desorption Ionization 218
3.1.2 Electrospray Ionization 222" V. B# c( G2 G# ]! r* p, g+ k' j
3.2 Ion Separation 225- y/ [7 {1 |( `" q7 X. Y
3.2.1 Time-of-Flight Analyzer 225- F( ^; \3 G8 k8 S
3.2.2 Triple Quadrupole Analyzer 227$ t4 A5 ]3 [% z, t1 }
3.2.3 Quadrupole Ion Trap 228
3.2.4 Quadrupole Time-of-Flight 230
3.2.5 Hybrid Triple Quadrupole Linear Ion Trap 2313 L, L/ X1 W: T8 {0 V
3.2.6 TOF/TOF Analyzer 2316 i! [* R+ A4 v$ a7 c7 _3 `% b3 ^3 j" [& ?
3.2.7 Fourier Transform Ion Cyclotron 232
3.2.8 Orbitrap 233
3.3 Generating MS Data for Protein Identification 233, q. v7 y: [4 G  ~1 ]
3.3.1 Peptide Mass Fingerprint 234
3.3.2 Peptide Mass Fingerprint Combined With Composition6 x! c% s8 {3 G8 `5 ?+ K3 ^" p5 {
Information 237
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence
Information 238
3.3.4 Tandem Mass Spectrometry 242# z/ `! D; b* t& e+ O0 Z+ O
3.4 Protein Characterization 2583 U3 D- E0 m8 z
3.4.1 Phosphorylation Analysis 259' I! e, {4 u& A' M& L5 d5 B- c
3.4.2 Affinity Chromatography 260
3.4.3 Chemical Derivatization 261; I/ T/ i% p' a; Z  D
3.4.4 Glycosylation 263
3.5 Protein Quantification Using Mass Spectrometry 264
3.5.1 Stable Isotope Labeling Approaches 264" ]% n) V1 x$ b2 c5 B0 K
3.5.2 Isotope-coded Affinity Tags 265# R" v. {) E& `1 \0 Y
3.5.3 Stable Isotope Labeling with Amino Acids in Cell Culture 266
3.5.4 AQUA 267
3.5.5 iTRAQ 267$ W, b' v' V1 L  H$ W
3.5.6 Non-labeling Software Approaches 268- r* j6 R  s% w$ w" f7 Z8 O
3.6 MS Strategies 271
3.6.1 Bottom up Approach 271
3.6.2 Top down Approach 2723 ?6 i8 \5 O2 X2 ~/ ^3 o# x
4 Functional Proteomics: Studies of Protein–Protein Interactions 273' O' x2 c+ k- k( Q2 Q
4.1 Non-immunological Methods 273
4.1.1 Separation of Intact Multi-protein Complexes 273
4.1.2 Probing with Interaction Partners 273
4.1.3 Surface Plasmon Resonance 274
4.2 Antibody-based Techniques 2754 y& @+ W: F% [( I2 h! G2 [; V
4.2.1 Western Blotting and Dot Blots 275
4.2.2 Protein Microarrays 276
Part II: Practical Manual of Proteome Analysis 279( g. O! Q7 k7 Z/ M- V
Equipment, Consumables, Reagents 281
Step 1: Sample Preparation 287. |: y+ Q* X* P9 L3 h
Step 2: Fluorescence Difference Gel Electrophoresis 299) t, e) S: v0 K3 |- k: z3 R% N  H. t& \
Step 3: Isoelectric Focusing 309: m1 Z- X# c- C0 A/ ?
Step 4: SDS Polyacrylamide Gel Electrophoresis 3231 l; g6 X; V. B+ C- E# U4 y
Step 5: Scanning of Gels Containing Pre-labeled Proteins 357* d, g5 r( ^, f# R' \7 F6 q7 b
Step 6: Staining of Gels 361
Step 7: Image Analysis and Evaluation of DIGE Gels 3736 H$ r2 l3 M1 k* O/ [$ q; u
Step 8: Spot Excision 3837 h) D3 n# V# s# b" r2 y7 F* Z
Step 9: Sample Destaining 387
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! I/ m! `$ J) Q; {, k  b
Step 15: Preparing for a Database Search 407
Part III: Trouble Shooting 411: B1 t$ H4 N, b
1 Two-dimensional Electrophoresis 413
1.1 Sample Preparation 413/ O# v5 P" H4 ?. W* y# O, ?
1.2 Isoelectric focusing in IGPG strips 414, e0 l7 {; |) X2 [
1.3 SDS PAGE 416; Q7 U7 J5 m5 M. @" D
1.4 Staining 417% _, m$ @: h' S5 }6 o" P* }, m
1.5 DIGE Fluorescence Labeling 4187 ~. g) ]8 i# V5 o( f# [
1.6 Results in 2-D Electrophoresis 421
2 Mass Spectrometry 429
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