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Proteomics in Practice" K4 B# Q" h4 M* N6 v0 R
A Guide to Successful Experimental Design" A1 T( `# r1 u6 O$ Y4 S5 n

Abbreviations, Symbols, Units XV
Introduction 1
1 History 1, S6 ]# f2 _( v* {
2 Critical Points 8
2.1 Challenges of the Protein Samples 8* P! u$ m, k  r2 C; h
2.1 Challenges of the Analysis Systems 114 k5 A. d0 ]) x3 k. ~) T% B
3 Proteomics Strategies 12
3.1 Proteome Mapping 12
3.2 Differential Analysis 12# i" e$ e5 R7 V
3.3 Time Point Experiments 13+ k9 A" ~+ J: ~. j# \( B7 k
3.4 Verification of Targets or Biomarkers 13; g, c, A8 Z' E: }
3.5 Integration of Results into Biological Context 13
3.6 Systems Biology 13) o+ D2 M' y7 o$ v4 P1 g" u. D( b
4 Concept of Experimental Planning 14
4.1 Biological Replicates 14
4.2 Pooling of Samples: Yes or No? 14+ I% n, q# T% }8 |
4.3 Pre-fractionation of Samples: Yes or No? 14# f% M4 F# V( U7 t% a; k
4.4 Which is the Best Workflow to Start With? 15
Part I: Proteomics Technology9 m3 K2 w6 H. x, V6 d- u9 M" B
1 Electrophoretic Techniques 19
1.1 The Principle of Electrophoresis and Some Methodological
Background 19( o6 v* y# {: X1 G
1.1.1 Free Flow Electrophoretic Methods 208 \! ]# g% {/ t. A
1.1.2 Gels for Electrophoretic Techniques 212 D0 k& P  H- }3 H  c8 v: Q2 j+ Y
1.1.3 Electroendosmosis Effects 21, W- e$ \+ r9 N- S* _
1.2 Polyacrylamide Gel Electrophoresis 22

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; R; s7 [% z* |% _. V5 b$ G+ ]
1.3.1 Electrophoretic Transfer 36
1.3.2 Protein Detection on the Membrane 36' Q/ i; ?4 P" L2 M; L8 P- P% y- j
1.4 Isoelectric Focusing 38
1.4.1 Theoretical Background 39
1.4.2 Preparation of IEF Gels 44
1.4.3 Isoelectric Focusing in Proteomics 457 r1 o3 m. h$ d7 O" V0 g) R2 G
1.5 Two-dimensional Electrophoresis 53& g! R! @7 K9 ~- ]+ M- z0 A' y
1.5.1 Sample Preparation 53% X1 E% P# x: ?+ g' M, G" r
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! [7 r4 f) t& y: G# V
1.5.5 Detection of Protein Spots 1196 J1 l3 B3 T0 P0 _5 X/ e" p  |1 F1 Q
1.6 Image Analysis 125
1.6.1 Image Acquisition 125% K5 B1 C8 Z" O# ^6 h8 ]' K! W) A+ b
1.6.2 Image Analysis and Evaluation 1290 f* x5 r/ C4 j% J
1.6.3 Use of 2-D Electrophoresis Data 137: {+ d! S7 ?5 H) ]
1.7 Spot Handling 137* J, l, b  B% c. R3 N2 X) W/ U
1.7.1 Spot Picking 139
1.7.2 Protein Cleavage 1413 d/ E2 W9 h$ x6 I, t& X$ F# p
Liquid Chromatography Techniques 151
2.1 Basic Principles of Important Liquid Chromatography
Techniques 1511 }  Y( D; ?: Q8 R/ U5 B7 d  z% d% }
2.1.1 Ion Exchange Chromatography 153
2.1.2 Reversed Phase Chromatography 162/ y4 O0 G6 |5 o: u4 S6 C
2.1.3 Affinity Chromatography 1674 ~! Q& F% f# n& r8 J3 \, V5 b1 g
2.1.4 Gel Filtration 1723 H, v, |$ j& O  M7 t* B! |1 P
2.2 Strategic Approach and General Applicability 174
2.3 Liquid Chromatography Techniques and Applications in Proteome; K: U' ]5 Q1 U) d
Analysis 176
2.3.1 Peptide Separation 176
2.3.2 2DLC Peptide Separation 1791 J# E7 E5 f- V. [5 u' m5 I3 [
2.3.3 Affinity Chromatography and LC-MS/MS 187
2.3.4 Protein Pre-fractionation 189. g2 c+ w, C7 H5 i- A8 O3 a8 ~
2.4 Practical Considerations and Application of LC-based Protein
Pre-fractionation 194. N5 w% y9 @# p( D3 W
2.4.1 Sample Extraction and Preparation 196
2.4.2 Experimental Setup 197
2.4.3 Ion Exchange Chromatography and* l! ?: K0 a" S6 S; }. K6 g1 i
Protein Pre-fractionation 198
Contents, C& ]6 p# {+ q/ d* Y, [9 z
2.4.4 Reversed Phase Chromatography and. |# N6 q& ~. _( h
Protein Pre-fractionation 205
2.4.5 Fraction Size and Number of Fractions 210
2.5 Critical Review and Outlook 211
3 Mass Spectrometry 215, d( ]/ B8 i3 S/ k( \/ ?
3.1 Ionization 218" v  b1 V+ }) b* d6 Z& J
3.1.1 Matrix Assisted Laser Desorption Ionization 218) w8 W7 r3 }8 D2 d; ?8 P
3.1.2 Electrospray Ionization 222# q: ^7 Q% m! k9 B5 l$ A+ b* ?  ?
3.2 Ion Separation 225$ G: J5 [+ @/ h% C5 N7 D
3.2.1 Time-of-Flight Analyzer 225. j# a' e/ r& n# w( N
3.2.2 Triple Quadrupole Analyzer 227
3.2.3 Quadrupole Ion Trap 228
3.2.4 Quadrupole Time-of-Flight 230
3.2.5 Hybrid Triple Quadrupole Linear Ion Trap 231
3.2.6 TOF/TOF Analyzer 2318 Z( J& G' K) z$ V
3.2.7 Fourier Transform Ion Cyclotron 2329 h) x6 t* Q! {, l
3.2.8 Orbitrap 233
3.3 Generating MS Data for Protein Identification 233; Y8 A6 H4 Y0 X6 L" [' Z) s
3.3.1 Peptide Mass Fingerprint 234
3.3.2 Peptide Mass Fingerprint Combined With Composition
Information 237( |9 {* p) C* s% N, L' d2 s
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence
Information 238
3.3.4 Tandem Mass Spectrometry 242
3.4 Protein Characterization 258) R4 T# F/ A# R. u/ X
3.4.1 Phosphorylation Analysis 259
3.4.2 Affinity Chromatography 2600 d9 C$ y% w5 L
3.4.3 Chemical Derivatization 261- g" N, x' H: ^! H7 U8 t$ |
3.4.4 Glycosylation 263
3.5 Protein Quantification Using Mass Spectrometry 264
3.5.1 Stable Isotope Labeling Approaches 264% n3 u& h  \1 I6 f" ?4 ^
3.5.2 Isotope-coded Affinity Tags 265& M, t  E" S: @3 I! p6 r
3.5.3 Stable Isotope Labeling with Amino Acids in Cell Culture 2665 p- L  p8 l) z0 ~& Q
3.5.4 AQUA 267
3.5.5 iTRAQ 267; {1 l0 E# G$ G( Y( B
3.5.6 Non-labeling Software Approaches 2688 E% q# D+ g3 ]. m" J
3.6 MS Strategies 271
3.6.1 Bottom up Approach 271
3.6.2 Top down Approach 272
4 Functional Proteomics: Studies of Protein–Protein Interactions 273
4.1 Non-immunological Methods 273" ^7 \! O1 G- a2 \. J0 J' `7 o! x
4.1.1 Separation of Intact Multi-protein Complexes 2731 B, h% s3 S1 }! z( e$ I
4.1.2 Probing with Interaction Partners 273
4.1.3 Surface Plasmon Resonance 274
4.2 Antibody-based Techniques 275
4.2.1 Western Blotting and Dot Blots 275
4.2.2 Protein Microarrays 2763 J7 Z4 m! Q3 @; ^' q" _2 i6 B
Part II: Practical Manual of Proteome Analysis 279
Equipment, Consumables, Reagents 281
Step 1: Sample Preparation 287# g2 E* [0 y2 o' Q) }) z
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. V8 O9 M6 H& p1 V+ w" w; K
Step 6: Staining of Gels 361" R* B3 S3 P0 k. D7 U
Step 7: Image Analysis and Evaluation of DIGE Gels 3735 K7 y& g0 L( g
Step 8: Spot Excision 383' p$ A  c) C! |* z: T  Q8 Q% Q- r- B
Step 9: Sample Destaining 387& V- M+ X2 S9 E7 }3 [
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% l5 v2 p+ A/ ?1 e
Step 14: Calibration of MALDI-ToF MS 403
Step 15: Preparing for a Database Search 407
Part III: Trouble Shooting 4116 M% y. e5 V  v, j& S9 x* B$ P
1 Two-dimensional Electrophoresis 4136 C1 t4 \# J4 i/ h9 e
1.1 Sample Preparation 413
1.2 Isoelectric focusing in IGPG strips 4148 F! i  L. a- |; _: O
1.3 SDS PAGE 416
1.4 Staining 417& _7 l% d3 V, V3 w2 ~! A
1.5 DIGE Fluorescence Labeling 418
1.6 Results in 2-D Electrophoresis 421
2 Mass Spectrometry 429

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