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 Practice2 `& M' b' b6 g% }
A Guide to Successful Experimental Design
5 X/ k4 M" W) a* H' `$ \
Abbreviations, Symbols, Units XV
Introduction 19 m% U4 _7 h% H; |/ N3 y
1 History 1
2 Critical Points 8) h0 I4 D' |6 G% p& @; N
2.1 Challenges of the Protein Samples 8
2.1 Challenges of the Analysis Systems 11
3 Proteomics Strategies 127 P2 y2 t" \5 K- h) z
3.1 Proteome Mapping 12& f. j7 t$ C, }2 V/ ~9 p
3.2 Differential Analysis 12( k9 T+ Y9 d9 h0 Q% q" o
3.3 Time Point Experiments 13
3.4 Verification of Targets or Biomarkers 13
3.5 Integration of Results into Biological Context 13% S( x( ~9 p# c" I# B( k8 a
3.6 Systems Biology 13
4 Concept of Experimental Planning 14
4.1 Biological Replicates 14
4.2 Pooling of Samples: Yes or No? 14
4.3 Pre-fractionation of Samples: Yes or No? 14" z( l; Y1 ?, `, v
4.4 Which is the Best Workflow to Start With? 15
Part I: Proteomics Technology, l- G* r8 J2 q% X; \! Y' K
1 Electrophoretic Techniques 19/ d" V% p2 @6 X- n/ ]
1.1 The Principle of Electrophoresis and Some Methodological+ \* m: K8 r* x9 @
Background 190 K5 x) Z, V/ D: c- _
1.1.1 Free Flow Electrophoretic Methods 20
1.1.2 Gels for Electrophoretic Techniques 210 N4 a1 h$ ?- Z
1.1.3 Electroendosmosis Effects 21
1.2 Polyacrylamide Gel Electrophoresis 22+ l9 k+ x9 Z8 @" Y5 _

1.2.1 The Polyacrylamide Gel 223 l8 }) `5 F6 K# m/ ]
1.2.2 SDS Polyacrylamide Gel Electrophoresis 276 ~: G6 W8 O+ `. ?% z* Z/ k# O
1.2.3 Blue Native Electrophoresis 32
1.2.4 Cationic Detergent Electrophoresis 34* f% ^( ], y% \& T. b! [+ s' }4 H
1.3 Blotting 351 j% h. \- a$ a( k7 L7 v
1.3.1 Electrophoretic Transfer 36" w. P* x( O' i. e" K
1.3.2 Protein Detection on the Membrane 36# s' B# u, u3 }$ X+ s6 T
1.4 Isoelectric Focusing 38" n2 m0 r8 ?8 ?; Z$ U
1.4.1 Theoretical Background 395 v  G; {- L. N5 l
1.4.2 Preparation of IEF Gels 446 s4 E1 _8 ~4 J+ ]) _0 c
1.4.3 Isoelectric Focusing in Proteomics 45' d1 w. Z  S; Z! Z( E/ O, F4 p
1.5 Two-dimensional Electrophoresis 53: ~# p) c5 ^& ?2 z
1.5.1 Sample Preparation 53
1.5.2 Pre-labeling of Proteins for Difference Gel Electrophoresis 68
1.5.3 First Dimension: Isoelectric Focusing in IPG Strips 77: Z: z9 j" _; `" w
1.5.4 Second Dimension: SDS Electrophoresis 1000 @; i8 F! \# Y
1.5.5 Detection of Protein Spots 119: A8 |  M! k! d4 J' j/ \. F
1.6 Image Analysis 1251 d9 p: S( [6 i3 B" P6 j6 W
1.6.1 Image Acquisition 1255 C6 h& `! T) I6 ?
1.6.2 Image Analysis and Evaluation 129+ P1 u: ~4 h/ H0 b! f7 F- u& X5 S. c
1.6.3 Use of 2-D Electrophoresis Data 137
1.7 Spot Handling 1372 I* y6 L9 r; ~4 S. ]6 A' b% P
1.7.1 Spot Picking 1395 M+ K* ?, y4 n: ]* a3 ?+ O
1.7.2 Protein Cleavage 141' j8 f* r/ }4 }
Liquid Chromatography Techniques 1511 R, Z9 _; r* l( {
2.1 Basic Principles of Important Liquid Chromatography9 ^0 Z+ P3 D& C* p' E. S+ B* W
Techniques 151: U2 O  ~4 O0 a. _
2.1.1 Ion Exchange Chromatography 153- s" n  p4 ]( a7 a8 \
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 1745 y& K) r$ {& d* u" F3 O' _9 }
2.3 Liquid Chromatography Techniques and Applications in Proteome
Analysis 176
2.3.1 Peptide Separation 1762 }) W* _- Q; o
2.3.2 2DLC Peptide Separation 179; [3 ^3 H2 Z; i  k5 D- L/ n
2.3.3 Affinity Chromatography and LC-MS/MS 187
2.3.4 Protein Pre-fractionation 189
2.4 Practical Considerations and Application of LC-based Protein
Pre-fractionation 194
2.4.1 Sample Extraction and Preparation 1968 U0 O) V# f1 U  \" ^
2.4.2 Experimental Setup 197
2.4.3 Ion Exchange Chromatography and
Protein Pre-fractionation 198; u1 t' x, p* k; P& e
Contents
2.4.4 Reversed Phase Chromatography and
Protein Pre-fractionation 205
2.4.5 Fraction Size and Number of Fractions 210
2.5 Critical Review and Outlook 2112 q; P. K- \: O6 K: u' {, V" r
3 Mass Spectrometry 215
3.1 Ionization 2181 |. U0 S* k1 m
3.1.1 Matrix Assisted Laser Desorption Ionization 218+ j0 i  \/ v& @4 Q- i  L+ p; n3 b, K0 `; G
3.1.2 Electrospray Ionization 2228 ?7 Z6 f/ q. |) M- S
3.2 Ion Separation 2253 Y9 |5 ~: K# b; W* a$ q
3.2.1 Time-of-Flight Analyzer 225
3.2.2 Triple Quadrupole Analyzer 227& d0 b5 ^) J" D2 i2 W4 V
3.2.3 Quadrupole Ion Trap 228  [$ P# x% H( C7 T
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, c6 g0 |% n, f7 |- ~% d
3.2.7 Fourier Transform Ion Cyclotron 2328 o0 Z3 T8 T3 Y! I/ a
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, a8 o5 B8 n+ r# R
Information 237  y. K8 r: Y* z; |$ T
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence
Information 2389 p4 o4 i2 h+ Y6 ]+ ?; g$ q/ W
3.3.4 Tandem Mass Spectrometry 242  J, x+ i# `2 A! i' [2 A7 j% ]
3.4 Protein Characterization 258  x8 j1 U, A4 v( u. E
3.4.1 Phosphorylation Analysis 259: C, _9 ]! @4 l
3.4.2 Affinity Chromatography 260! @2 [2 n" o& I6 s* a5 o
3.4.3 Chemical Derivatization 261# i5 z  I  y' v% C
3.4.4 Glycosylation 263
3.5 Protein Quantification Using Mass Spectrometry 264
3.5.1 Stable Isotope Labeling Approaches 264
3.5.2 Isotope-coded Affinity Tags 265
3.5.3 Stable Isotope Labeling with Amino Acids in Cell Culture 266
3.5.4 AQUA 267
3.5.5 iTRAQ 2674 B- k) c+ Y5 o' E0 g" O
3.5.6 Non-labeling Software Approaches 268; t, C& M* I. ^$ E1 o' I# k+ H
3.6 MS Strategies 271
3.6.1 Bottom up Approach 271: e4 a1 Z. b8 s$ Z! u; j
3.6.2 Top down Approach 272
4 Functional Proteomics: Studies of Protein–Protein Interactions 273+ v- ~4 D9 z( N- N/ Z% c! L. L
4.1 Non-immunological Methods 273. [  ?- t% {& }0 \7 g
4.1.1 Separation of Intact Multi-protein Complexes 273' E+ ^# S" N0 I+ v& k3 ]: @: U
4.1.2 Probing with Interaction Partners 273$ \3 e8 g2 l5 M% L& C- B* ]- \  \
4.1.3 Surface Plasmon Resonance 2741 Q" e: N& R: `' m7 ~) n1 Z
4.2 Antibody-based Techniques 275
4.2.1 Western Blotting and Dot Blots 275
4.2.2 Protein Microarrays 276
Part II: Practical Manual of Proteome Analysis 279
Equipment, Consumables, Reagents 281
Step 1: Sample Preparation 2877 s1 v5 [! {/ ]* m$ C
Step 2: Fluorescence Difference Gel Electrophoresis 299. n! n6 L! G; z7 n2 ^6 Y4 a' f0 H
Step 3: Isoelectric Focusing 309
Step 4: SDS Polyacrylamide Gel Electrophoresis 323
Step 5: Scanning of Gels Containing Pre-labeled Proteins 3577 L: G, e& `  J* i( e1 g1 [
Step 6: Staining of Gels 361
Step 7: Image Analysis and Evaluation of DIGE Gels 373
Step 8: Spot Excision 383
Step 9: Sample Destaining 387/ C5 G9 d" k! b# n& m
Step 10: Protein Digestion 389! }4 A! i4 S' j' Q3 o! E
Step 11: Microscale Desalting and Concentrating of Sample 393
Step 12: Chemical Derivatization of the Peptide Digest 3970 g( u: {! o; S, T4 M( K) S: l, f
Step 13: MS Analysis 399
Step 14: Calibration of MALDI-ToF MS 403+ j3 u2 T# |! `: e# l( G3 M
Step 15: Preparing for a Database Search 407$ ]* e, {3 q% i# h
Part III: Trouble Shooting 411# u( _# z- p/ j
1 Two-dimensional Electrophoresis 413
1.1 Sample Preparation 413
1.2 Isoelectric focusing in IGPG strips 414
1.3 SDS PAGE 416
1.4 Staining 417
1.5 DIGE Fluorescence Labeling 418: M. B+ i4 z0 @6 k; z
1.6 Results in 2-D Electrophoresis 4218 i8 i2 m. v" J. v, }
2 Mass Spectrometry 429" u1 @+ \. |9 L, {" w0 h" g

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