PDF电子书：Gel-Free Proteomics

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; T3 }0 |, a- O! h, Z2 E$ ^) i* wGel-Free Proteomics
4 L) c: O3 E. I5 c: qContents/ }+ b& E. m4 I& h, L4 r8 A
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v9 f# E/ S: B. ~1 h
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
' h6 n% x0 G/ `! M6 R1. Mass Spectrometry-Driven Proteomics: An Introduction . . . . . . . . . . . . . 1/ I4 M$ K$ D# o+ C& P4 M
Kenny Helsens, Lennart Martens, Joël Vandekerckhove,
9 a9 r3 W5 |" I3 V* C8 v) Vand Kris Gevaert! \, }& C# ^* k! Y  w
2. Metabolic Labeling of Model Organisms Using Heavy Nitrogen (15N) . . . . . . 29
- ?! Q+ `' B' b- L2 ?% N! R" WJoost W. Gouw, Bastiaan B.J. Tops, and Jeroen Krijgsveld
3 o+ r  n& h1 T4 j3. Trypsin-Catalyzed Oxygen-18 Labeling for Quantitative Proteomics . . . . . . . 43
3 H( f& I% S+ {- q3 AWei-Jun Qian, Brianne O. Petritis, Carrie D. Nicora,+ b' K( c6 B7 p
and Richard D. Smith
0 i2 G6 V5 H7 Y/ }& i+ H4. ICPL Labeling Strategies for Proteome Research . . . . . . . . . . . . . . . . . 55
* {1 l% G+ u0 U5 r7 JFriedrich Lottspeich and Josef Kellermann& d5 t  s4 q! y5 k  G: \
5. Quantitative Proteome Analysis Using Isobaric Peptide Termini
  q/ V6 T, P( ^4 h% DLabeling (IPTL) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
5 j, b% f0 j1 I* _  g3 B1 uMagnus Ø. Arntzen, Christian J. Koehler, Achim Treumann, and Bernd Thiede
+ X6 _$ D! o* G  Q3 L6. Complete Chemical Modification of Amine and Acid Functional Groups
: I9 y# m# i' l' s, N  gof Peptides and Small Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
2 P* e" \; r( N- xCasey J. Krusemark, Brian L. Frey, Lloyd M. Smith, and Peter J. Belshaw% [. O7 v5 `0 L3 s6 K
7. Production and Use of Stable Isotope-Labeled Proteins for Absolute
+ o# I2 m3 }0 |8 r" l: V' P6 @; rQuantitative Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93! m" C" O) o, _0 W; S+ w( Q
Dorothée Lebert, Alain Dupuis, Jérôme Garin, Christophe Bruley,3 E! |! Y) @9 v6 c/ X1 L. x
and Virginie Brun! L% `7 `# r& X2 c5 }. F
8. Organelle Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1172 ?5 ^0 \8 D8 m2 J% E
Sophie Duclos and Michel Desjardins
4 ^1 n/ ]5 E  V/ e( h9. Membrane Protein Digestion – Comparison of LPI HexaLane- B1 j* I1 P0 H0 ?  H
with Traditional Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
) v/ e; J: u: Q0 nPing Sui, Tasso Miliotis, Max Davidson, Roger Karlsson, and Anders Karlsson# q3 C- f/ b4 L
10. GeLCMS for In-Depth Protein Characterization and Advanced Analysis3 K$ L3 H; J" W) f& C  y( {5 }" H' B: z
of Proteomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143/ ?! z. }( c4 S5 o' s+ Q* e7 @
Alicia Lundby and Jesper V. Olsen
$ R$ H& V! Y4 X0 \, g11. Exploring New Proteome Space: Combining Lys-N Proteolytic Digestion
; _$ j! m; x1 c6 P- S3 _and Strong Cation Exchange (SCX) Separation in Peptide-Centric# m" M3 i% S, \* y! c; d+ g2 D
MS-Driven Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
) `6 x. U: z5 @6 X# V0 Y# [( |12. Quantitation of Newly Synthesized Proteins by Pulse Labeling5 c2 H0 O' V8 ?: c  }! D9 B
with Azidohomoalanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
% ?3 V$ M  S0 m: {) G4 A0 x' ?+ c) OGertjan Kramer, Piotr T. Kasper, Luitzen de Jong, and Chris G. de Koster" ^, m+ }3 u+ w4 t; E0 L
13. Analytical Strategies in Mass Spectrometry-Based Phosphoproteomics . . . . . . . 183
5 Q3 [8 g/ _. P7 ]& Q6 e" }# [% ZHeidi Rosenqvist, Juanying Ye, and Ole N. Jensen/ B& x/ e+ n# g! N' f7 T3 l2 k
14. A Protocol on the Use of Titanium Dioxide Chromatography0 L4 h- Z- j+ q6 `
for Phosphoproteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2151 e! k3 Y+ ^: L- ?- i: [. e7 B) ~& k
Martijn W.H. Pinkse, Simone Lemeer, and Albert J.R. Heck
7 h& ^. G- O  \% N0 d) P15. Positional Proteomics at the N-Terminus as a Means of Proteome Simplification . 229
* h# h4 P! r3 x  y" GGemma R. Davidson, Stuart D. Armstrong, and Robert J. Beynon( h5 L) |% G. f$ U
16. N-Terminomics: A High-Content Screen for Protease Substrates
% K. R# K. g+ x$ {and Their Cleavage Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
- [. M% l5 D- k; R: Y+ q; LJohn C. Timmer and Guy S. Salvesen
; f" ?: U1 D: ~17. Protease Specificity Profiling by Tandem Mass Spectrometry Using
' v3 k& f4 T' H- E1 y. C+ LProteome-Derived Peptide Libraries . . . . . . . . . . . . . . . . . . . . . . . . 257
* \" g% }$ v. _; z# WOliver Schilling, Ulrich auf dem Keller, and Christopher M. Overall' r( I' f/ c& G) D* e4 d' P% c
18. Identification of Proteolytic Products and Natural Protein N-Termini
& V7 d. v  J' e& J2 `3 v2 Cby Terminal Amine Isotopic Labeling of Substrates (TAILS) . . . . . . . . . . . . 273
$ B5 S  n; X0 V$ H' QAlain Doucet, Oded Kleifeld, Jayachandran N. Kizhakkedathu,# [" i) D8 q/ Z# T
and Christopher M. Overall" Y) v8 Q0 @2 K& w; _# T2 z
19. Lectins as Tools to Select for Glycosylated Proteins . . . . . . . . . . . . . . . . 289& h1 D! x6 o% }6 f0 ~. u$ o
Els J.M. Van Damme+ I: x9 l4 B2 }8 H  N3 r. q% A1 A6 x
20. Strong Cation Exchange Chromatography for Analysis of Sialylated Glycopeptides 299
% l& Y5 q& }5 H% ~1 q' q2 ~Katharina Lohrig, Albert Sickmann, and Urs Lewandrowski
3 l) X: z0 T6 s( E) d21. Titanium Dioxide Enrichment of Sialic Acid-Containing Glycopeptides . . . . . . 309
6 ?. S4 B$ x- Q: hGiuseppe Palmisano, Sara E. Lendal, and Martin R. Larsen" v; w% E# A3 M* D2 h
22. Chemical De-O-glycosylation of Glycoproteins for Applications
& q5 z( x8 O' L. Hin LC-Based Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
0 `7 {; I% W& Y6 V% QFranz-Georg Hanisch
' N- j3 t/ m7 t; j23. Ubiquitination and Degradation of Proteins . . . . . . . . . . . . . . . . . . . . 335* q/ i4 X; q- e. c. I' V( S2 l
Yelena Kravtsova-Ivantsiv and Aaron Ciechanover( o2 S% i5 a4 b5 l; d6 c5 D
24. Bioinformatics Challenges in Mass Spectrometry-Driven Proteomics . . . . . . . 359
! V/ D) ]/ p! lLennart Martens, p( I( i( A6 q% `
25. A Case Study on the Comparison of Different Software Tools
, F6 f& _* e, [for Automated Quantification of Peptides . . . . . . . . . . . . . . . . . . . . . 3736 ~' d2 a& Z$ Q0 v8 `8 }$ w
Niklaas Colaert, Joël Vandekerckhove, Lennart Martens,5 g+ |" g, Q4 a5 y
and Kris Gevaert0 \& Z# \4 d% i/ P' h3 t* e5 n
Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399" {; z  H+ ~/ W
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