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Proteomics in Practice
A Guide to Successful Experimental Design
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Abbreviations, Symbols, Units XV5 V- D/ ^  l; d
Introduction 1
1 History 1
2 Critical Points 8& P8 q  Q- }. W2 o2 ^
2.1 Challenges of the Protein Samples 8
2.1 Challenges of the Analysis Systems 11& ]9 X0 O: k% [: L! y% j  i& Y
3 Proteomics Strategies 12& s( G( z! v; ]% x: G- I% {
3.1 Proteome Mapping 12
3.2 Differential Analysis 128 m) @4 Z* u7 J6 n
3.3 Time Point Experiments 136 y+ b4 Z0 P8 l6 A9 F) x8 z( }
3.4 Verification of Targets or Biomarkers 13/ C9 a( y# l( }7 Z4 F' G7 ^6 h
3.5 Integration of Results into Biological Context 133 G  c3 O0 Y  {8 b9 b
3.6 Systems Biology 13
4 Concept of Experimental Planning 148 r! }& Q* [+ T( J
4.1 Biological Replicates 14" Z  A2 r8 k. A+ S* R
4.2 Pooling of Samples: Yes or No? 14( y1 J  w" d! h; \1 Y# |- E6 J
4.3 Pre-fractionation of Samples: Yes or No? 14
4.4 Which is the Best Workflow to Start With? 159 r) j* J3 _# N4 b9 l  ]  d
Part I: Proteomics Technology
1 Electrophoretic Techniques 198 ?/ T" R6 v2 [  ~
1.1 The Principle of Electrophoresis and Some Methodological% M6 T; d9 P% s9 a3 Y$ d
Background 19
1.1.1 Free Flow Electrophoretic Methods 20
1.1.2 Gels for Electrophoretic Techniques 21
1.1.3 Electroendosmosis Effects 21& u6 e/ g$ J* ?' x
1.2 Polyacrylamide Gel Electrophoresis 223 p: e& \* L3 H' G% R; E" `- \
" _( k% q4 x: f1 y" D0 p2 {2 Y
1.2.1 The Polyacrylamide Gel 22# d+ D# D. F- S
1.2.2 SDS Polyacrylamide Gel Electrophoresis 270 Z5 J1 y0 z2 I; ]
1.2.3 Blue Native Electrophoresis 32
1.2.4 Cationic Detergent Electrophoresis 34
1.3 Blotting 35
1.3.1 Electrophoretic Transfer 36( i) d3 g* S- h* ?) t3 r
1.3.2 Protein Detection on the Membrane 369 `3 l! }3 {" o6 \4 w
1.4 Isoelectric Focusing 38' [, f3 ]3 n  T, Y, A$ [& Y
1.4.1 Theoretical Background 39" W! L+ s4 c$ E6 W3 U1 ^4 i: I
1.4.2 Preparation of IEF Gels 444 b3 C/ K+ p/ c; t4 J
1.4.3 Isoelectric Focusing in Proteomics 45
1.5 Two-dimensional Electrophoresis 53
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
1.5.4 Second Dimension: SDS Electrophoresis 100
1.5.5 Detection of Protein Spots 119
1.6 Image Analysis 125( G! d" ]3 S3 E; z9 ?; C( R
1.6.1 Image Acquisition 125
1.6.2 Image Analysis and Evaluation 1297 Z/ x: _& B0 W  U3 m
1.6.3 Use of 2-D Electrophoresis Data 1374 U0 n+ |: k) M9 X5 a$ ~( B2 A. j
1.7 Spot Handling 137
1.7.1 Spot Picking 139( f) g" q5 i: M9 j  o" G9 _
1.7.2 Protein Cleavage 141
Liquid Chromatography Techniques 1515 A2 Q7 N9 K4 S
2.1 Basic Principles of Important Liquid Chromatography1 Y/ f1 O2 W& T2 m  j
Techniques 151
2.1.1 Ion Exchange Chromatography 153
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 174) e/ u+ W% W- U, V- G" n5 |. U
2.3 Liquid Chromatography Techniques and Applications in Proteome# Q" a4 R9 \# A2 H' S
Analysis 1767 A0 o8 S$ o$ e7 C
2.3.1 Peptide Separation 1763 n: S4 `: ]- G/ D8 P) O, k
2.3.2 2DLC Peptide Separation 1791 ~" n1 h  O* W1 s" Y5 x
2.3.3 Affinity Chromatography and LC-MS/MS 187- N- t4 T: s( H+ d  g
2.3.4 Protein Pre-fractionation 189) T! _4 S( \' V8 b# T
2.4 Practical Considerations and Application of LC-based Protein
Pre-fractionation 194
2.4.1 Sample Extraction and Preparation 1964 U- N6 w4 Y# W  ~  ^( x9 T' y
2.4.2 Experimental Setup 197/ D  P# k0 Y$ ~
2.4.3 Ion Exchange Chromatography and8 A' \+ j* i) e6 W. b* c
Protein Pre-fractionation 198, @8 ^0 K) `  K" c
Contents7 |# w& J: D5 y% r4 f/ B# a
2.4.4 Reversed Phase Chromatography and1 ]% {! e2 X7 R6 ?2 ?8 W
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
3.1 Ionization 218: d* B4 y' ^$ M: R5 T( e# V
3.1.1 Matrix Assisted Laser Desorption Ionization 218
3.1.2 Electrospray Ionization 222) @+ i0 _, c3 _7 k4 w  o
3.2 Ion Separation 225' Z5 L0 s$ q4 ~6 [
3.2.1 Time-of-Flight Analyzer 225; K! C6 G; W4 _6 _
3.2.2 Triple Quadrupole Analyzer 227
3.2.3 Quadrupole Ion Trap 228  X' A: z* l" I0 G5 t7 f( i
3.2.4 Quadrupole Time-of-Flight 230
3.2.5 Hybrid Triple Quadrupole Linear Ion Trap 231/ d0 g* Z1 L9 B. e, c, K
3.2.6 TOF/TOF Analyzer 231
3.2.7 Fourier Transform Ion Cyclotron 2328 ]8 l0 A" X" g) ?) u
3.2.8 Orbitrap 233
3.3 Generating MS Data for Protein Identification 2339 @  V, e6 q% Q# h' _
3.3.1 Peptide Mass Fingerprint 2349 f- M* Q% j4 O- j& \8 f! ]  ?
3.3.2 Peptide Mass Fingerprint Combined With Composition" x! w0 C- I1 i  j; s
Information 237
3.3.3 Peptide Mass Fingerprint Combined With Partial Sequence+ u$ `( ^% r& E0 e# w
Information 238. H* u+ g- p% h+ e% n
3.3.4 Tandem Mass Spectrometry 242
3.4 Protein Characterization 258
3.4.1 Phosphorylation Analysis 259
3.4.2 Affinity Chromatography 260) D0 T. m0 T6 I# R
3.4.3 Chemical Derivatization 261& {) x! [, W) I8 B# y
3.4.4 Glycosylation 263' S9 e" R6 i' b, f; l. Z
3.5 Protein Quantification Using Mass Spectrometry 264- s% o: F' G& z! D% t  r$ X
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 2677 n" x1 m! J5 X1 G0 D/ B
3.5.5 iTRAQ 267  u& V7 k  Z' ?/ f; x
3.5.6 Non-labeling Software Approaches 268
3.6 MS Strategies 271
3.6.1 Bottom up Approach 271' M) H+ V2 C" x6 S7 B+ n- M
3.6.2 Top down Approach 272
4 Functional Proteomics: Studies of Protein–Protein Interactions 2739 ^0 B. @2 S2 O& B- _$ ^$ p$ t
4.1 Non-immunological Methods 2733 j, {# p" u+ {* S& k
4.1.1 Separation of Intact Multi-protein Complexes 273! V- l8 t1 Q, r; Y5 Z. g; e9 ^
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! V/ \& \3 H* i9 i+ v& W. p' f, M
4.2.2 Protein Microarrays 276
Part II: Practical Manual of Proteome Analysis 279
Equipment, Consumables, Reagents 281; p2 x% ^1 |* ]/ f  e" J
Step 1: Sample Preparation 287+ A& Z1 D! g+ S$ h) `8 o) y
Step 2: Fluorescence Difference Gel Electrophoresis 299# ^, `/ g2 ^- u3 X8 B5 G5 Q% u+ y
Step 3: Isoelectric Focusing 309
Step 4: SDS Polyacrylamide Gel Electrophoresis 323- G3 c7 B$ j- j0 \" `" i5 N
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& X* T) q* s- T- i, |8 w* ^! y% c
Step 8: Spot Excision 383
Step 9: Sample Destaining 387
Step 10: Protein Digestion 389+ {5 c' C: t7 w7 Y5 q7 N
Step 11: Microscale Desalting and Concentrating of Sample 3937 ^6 ~! a7 e( X+ j# w- Z  m
Step 12: Chemical Derivatization of the Peptide Digest 397, e3 y$ G* o! h8 p+ B9 p
Step 13: MS Analysis 399
Step 14: Calibration of MALDI-ToF MS 403: p9 A- e- x  N: z: j
Step 15: Preparing for a Database Search 407
Part III: Trouble Shooting 411; L5 I/ f% M" F% i: F7 I8 X
1 Two-dimensional Electrophoresis 413  X$ @  H6 Y- ^* v
1.1 Sample Preparation 413
1.2 Isoelectric focusing in IGPG strips 4144 _, K! m1 [, j8 K+ t# q
1.3 SDS PAGE 416/ l! G5 C; ?0 f7 ~% ~, ~  o! D
1.4 Staining 417
1.5 DIGE Fluorescence Labeling 4183 D% b( a5 I$ H+ D" M
1.6 Results in 2-D Electrophoresis 4217 K0 T. Z! {" T5 Y  m
2 Mass Spectrometry 4298 R8 W; e( ?9 _& k* f% R
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