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Proteomics in Practice6 r5 ^1 W0 G+ @! a1 z$ s
A Guide to Successful Experimental Design+ a4 ], [6 q& s- m' A
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Abbreviations, Symbols, Units XV: i( N, g( U) R; p- F
Introduction 1
1 History 1& o7 Z" O9 V. x. s8 p
2 Critical Points 8
2.1 Challenges of the Protein Samples 8
2.1 Challenges of the Analysis Systems 11" r9 x3 p; ~. T* x
3 Proteomics Strategies 124 L$ J1 N! v! V9 ?  _& p" V
3.1 Proteome Mapping 129 T) J6 c) O* j6 U$ J
3.2 Differential Analysis 12* Q$ T9 W5 R5 I+ u
3.3 Time Point Experiments 13) k2 |+ f. `& X: t5 @2 \2 d; u
3.4 Verification of Targets or Biomarkers 13
3.5 Integration of Results into Biological Context 139 t* z3 g7 t# B' x
3.6 Systems Biology 13
4 Concept of Experimental Planning 14& m% w- {3 k9 S9 v" ?, A
4.1 Biological Replicates 14
4.2 Pooling of Samples: Yes or No? 14
4.3 Pre-fractionation of Samples: Yes or No? 141 |% C* c( U5 C" c  N) I9 c/ e
4.4 Which is the Best Workflow to Start With? 15
Part I: Proteomics Technology
1 Electrophoretic Techniques 19- p- x0 y3 X, \7 A+ R( z
1.1 The Principle of Electrophoresis and Some Methodological+ D# J1 k' ^8 R
Background 19
1.1.1 Free Flow Electrophoretic Methods 20
1.1.2 Gels for Electrophoretic Techniques 21
1.1.3 Electroendosmosis Effects 219 n% t: [/ T! w2 ^% N. V5 U
1.2 Polyacrylamide Gel Electrophoresis 22

1.2.1 The Polyacrylamide Gel 221 R+ S6 ^$ D7 F  J1 \" i
1.2.2 SDS Polyacrylamide Gel Electrophoresis 272 z, Y1 O2 x* {% Q  P
1.2.3 Blue Native Electrophoresis 32
1.2.4 Cationic Detergent Electrophoresis 34
1.3 Blotting 35. J3 L9 o0 b/ L7 e" F
1.3.1 Electrophoretic Transfer 36
1.3.2 Protein Detection on the Membrane 36
1.4 Isoelectric Focusing 38% V3 V. q/ a3 x( Z" g8 n
1.4.1 Theoretical Background 39- S! n" d0 P" q3 `
1.4.2 Preparation of IEF Gels 445 J6 h5 P& m# E- w% X/ ?
1.4.3 Isoelectric Focusing in Proteomics 45' Y0 ^1 h$ a2 J9 j- [4 S$ ?
1.5 Two-dimensional Electrophoresis 53
1.5.1 Sample Preparation 53) m$ X5 o: C2 C
1.5.2 Pre-labeling of Proteins for Difference Gel Electrophoresis 68
1.5.3 First Dimension: Isoelectric Focusing in IPG Strips 772 {7 l; T( L" [+ R
1.5.4 Second Dimension: SDS Electrophoresis 1007 k. h( K/ b+ ^
1.5.5 Detection of Protein Spots 119. X4 a1 [& g1 p8 n, L2 e
1.6 Image Analysis 125
1.6.1 Image Acquisition 125- F9 c+ ~$ ~- u: p5 d3 z! s
1.6.2 Image Analysis and Evaluation 1290 r+ h7 l% b/ B
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 1417 |4 Y2 o1 x; }3 R) g& ]
Liquid Chromatography Techniques 151! Y$ z% K1 k4 T5 I+ \, I/ P
2.1 Basic Principles of Important Liquid Chromatography* X* p; i6 J. j$ R# f5 [5 p" y! u" ?
Techniques 151( {: {8 ~' B% ]4 s# O# F- ^4 i
2.1.1 Ion Exchange Chromatography 1537 F4 e% [. M, B* v4 r3 V
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 1742 |9 u0 J3 p' k! ^) E
2.3 Liquid Chromatography Techniques and Applications in Proteome: u7 Z) b& r2 z0 j
Analysis 176
2.3.1 Peptide Separation 1765 m; L1 G' h3 }( x6 i# }; ?: G
2.3.2 2DLC Peptide Separation 179( K; n! Z3 ~3 v* K
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. }- D7 p# F& t" L
Pre-fractionation 194
2.4.1 Sample Extraction and Preparation 196
2.4.2 Experimental Setup 197$ q1 N# x! ?3 s2 H- ~
2.4.3 Ion Exchange Chromatography and- j8 Y: N3 M: K
Protein Pre-fractionation 198
Contents, ~) Z% [( ^$ [5 P5 m5 z: J
2.4.4 Reversed Phase Chromatography and7 k: c6 d: J8 F; m, e8 a
Protein Pre-fractionation 205* e' H" g, A+ o% B2 A
2.4.5 Fraction Size and Number of Fractions 210
2.5 Critical Review and Outlook 211
3 Mass Spectrometry 215
3.1 Ionization 218
3.1.1 Matrix Assisted Laser Desorption Ionization 2180 x5 I* U, m. \+ i5 \  A. ^
3.1.2 Electrospray Ionization 222
3.2 Ion Separation 225  l: x! W# V1 k, _9 G8 e. s
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 230% w/ `; V1 x; n# y
3.2.5 Hybrid Triple Quadrupole Linear Ion Trap 231$ U+ n/ v4 ?1 I% L% {
3.2.6 TOF/TOF Analyzer 231
3.2.7 Fourier Transform Ion Cyclotron 232" l& W, ~7 V4 D
3.2.8 Orbitrap 2334 Q' R6 L9 F7 Z& ]7 m
3.3 Generating MS Data for Protein Identification 233
3.3.1 Peptide Mass Fingerprint 2346 e- l- ]/ M0 T  h3 h
3.3.2 Peptide Mass Fingerprint Combined With Composition
Information 237
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence
Information 238
3.3.4 Tandem Mass Spectrometry 242
3.4 Protein Characterization 258* T8 o# s2 B; o% x# S; O
3.4.1 Phosphorylation Analysis 2592 X& A. m* }$ j
3.4.2 Affinity Chromatography 260
3.4.3 Chemical Derivatization 261
3.4.4 Glycosylation 2635 g# H) h% W- e3 N) J4 @. u% J
3.5 Protein Quantification Using Mass Spectrometry 264
3.5.1 Stable Isotope Labeling Approaches 264( v7 H) A; w7 F! t
3.5.2 Isotope-coded Affinity Tags 265
3.5.3 Stable Isotope Labeling with Amino Acids in Cell Culture 2667 I0 S% \# G8 ?! R! V
3.5.4 AQUA 267
3.5.5 iTRAQ 2670 f$ A! e" T' h3 Y. q0 e( q
3.5.6 Non-labeling Software Approaches 268+ d9 S5 s% b4 a  G
3.6 MS Strategies 271
3.6.1 Bottom up Approach 271$ W" d% d/ }3 v) \' g; o
3.6.2 Top down Approach 2727 b' G) w) L) `' Z6 a# h  Y1 V$ U
4 Functional Proteomics: Studies of Protein–Protein Interactions 273
4.1 Non-immunological Methods 273' k  k5 m$ l! m, K
4.1.1 Separation of Intact Multi-protein Complexes 273% y, n. }) g% B8 B3 j6 F/ F
4.1.2 Probing with Interaction Partners 273
4.1.3 Surface Plasmon Resonance 274# M0 v0 ?9 u2 b8 {
4.2 Antibody-based Techniques 2753 ?6 `, c9 @  o+ T4 G
4.2.1 Western Blotting and Dot Blots 2753 Y3 p- R0 Q3 l
4.2.2 Protein Microarrays 276* a3 K5 K5 N, V) B; }0 Y
Part II: Practical Manual of Proteome Analysis 2790 R/ _% k& W; ^; I) Z$ ~7 g
Equipment, Consumables, Reagents 281% d/ o# t5 [5 B, V$ ~& T( S/ `
Step 1: Sample Preparation 287
Step 2: Fluorescence Difference Gel Electrophoresis 299$ _  p; z% [' t/ A4 _
Step 3: Isoelectric Focusing 3093 \( R" `4 R$ ^) D: [
Step 4: SDS Polyacrylamide Gel Electrophoresis 323
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 383
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
Step 15: Preparing for a Database Search 407' G% w3 ~) x* T7 G2 F* m9 R; J; v
Part III: Trouble Shooting 411
1 Two-dimensional Electrophoresis 413; ?* J  z) A& d6 p+ q3 |
1.1 Sample Preparation 413
1.2 Isoelectric focusing in IGPG strips 414
1.3 SDS PAGE 4161 L1 G* O/ i# d  ~: h6 T$ f! Z
1.4 Staining 417
1.5 DIGE Fluorescence Labeling 418
1.6 Results in 2-D Electrophoresis 421) Z! X! b' f* C2 K
2 Mass Spectrometry 429
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