PDF电子书：Gel-Free Proteomics

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% w; J9 r, H! Y8 {; W, t* B7 @2 m7 E  XGel-Free Proteomics" d# ]4 @( S: G+ b( L5 s) w
Contents( b) W6 R+ `. H! o* W+ W9 O/ P
Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
% R* P  S* Q0 u* \Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
4 M' P" S' ]& J& e1 ^) l1. Mass Spectrometry-Driven Proteomics: An Introduction . . . . . . . . . . . . . 1& X+ S8 B( {; A+ @; a
Kenny Helsens, Lennart Martens, Joël Vandekerckhove,1 B8 a2 L% M3 |& ?. ?' e
and Kris Gevaert
! ~9 s" q$ C! L; R5 X  f, I2. Metabolic Labeling of Model Organisms Using Heavy Nitrogen (15N) . . . . . . 291 X& c8 l3 p8 h+ ]6 w1 C
Joost W. Gouw, Bastiaan B.J. Tops, and Jeroen Krijgsveld
" i. U0 y, P8 `/ `  `/ j3. Trypsin-Catalyzed Oxygen-18 Labeling for Quantitative Proteomics . . . . . . . 43
! {+ f0 R: `0 g+ i7 H9 P9 DWei-Jun Qian, Brianne O. Petritis, Carrie D. Nicora,. I) ?* t  Y: n  Q1 l8 r! f
and Richard D. Smith
" e3 U( F3 d. t* f1 ^4. ICPL Labeling Strategies for Proteome Research . . . . . . . . . . . . . . . . . 55
0 S3 j+ j2 ]' ]Friedrich Lottspeich and Josef Kellermann
7 b: G( {8 n' }" H5. Quantitative Proteome Analysis Using Isobaric Peptide Termini
$ S) d% A; f0 pLabeling (IPTL) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
, R2 C6 g: i! {' y4 c. ZMagnus Ø. Arntzen, Christian J. Koehler, Achim Treumann, and Bernd Thiede
- v" t4 a3 Y8 G: c7 H5 D6. Complete Chemical Modification of Amine and Acid Functional Groups/ _: ?' f2 i; J( Y: q6 o
of Peptides and Small Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . 778 k: ]4 T+ Z7 F8 o8 s) h
Casey J. Krusemark, Brian L. Frey, Lloyd M. Smith, and Peter J. Belshaw9 G4 B9 ?' n$ L+ K, d) p
7. Production and Use of Stable Isotope-Labeled Proteins for Absolute
7 c3 O( A& W5 F  ]1 w$ p) v7 t- X6 NQuantitative Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
) d- Q( y; P5 M9 t! |  JDorothée Lebert, Alain Dupuis, Jérôme Garin, Christophe Bruley,5 |1 U' `# M! b1 x
and Virginie Brun* Y+ A9 j+ {% z4 e1 G" m
8. Organelle Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117+ v; b7 E$ V( o0 e
Sophie Duclos and Michel Desjardins/ L% \& l" l4 k9 n
9. Membrane Protein Digestion – Comparison of LPI HexaLane7 D+ T& m' B0 w0 R
with Traditional Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129+ c' `7 \7 _4 [: X6 ?& _8 z2 _
Ping Sui, Tasso Miliotis, Max Davidson, Roger Karlsson, and Anders Karlsson7 n; J: @9 N' h8 Y: d4 }+ d
10. GeLCMS for In-Depth Protein Characterization and Advanced Analysis
" D. h- m2 q: F" Y0 Kof Proteomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143% y6 v; s& c. k' ~5 u
Alicia Lundby and Jesper V. Olsen
* ^- @7 |  P- w% R& E. N2 y3 w11. Exploring New Proteome Space: Combining Lys-N Proteolytic Digestion
, j8 e2 k8 ^% ?3 C! aand Strong Cation Exchange (SCX) Separation in Peptide-Centric
" B6 ]/ d5 k" I  eMS-Driven Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157* `# }5 Y2 ^5 B
12. Quantitation of Newly Synthesized Proteins by Pulse Labeling
- F5 a& K2 |0 }/ s" m7 b# \with Azidohomoalanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
6 V* A& N& i& R' B) p6 \) MGertjan Kramer, Piotr T. Kasper, Luitzen de Jong, and Chris G. de Koster
* x( {" S% L$ U4 u0 S13. Analytical Strategies in Mass Spectrometry-Based Phosphoproteomics . . . . . . . 1830 a; ~& y0 ?5 @- l8 p- [. x
Heidi Rosenqvist, Juanying Ye, and Ole N. Jensen
4 O* F% w( ?, T$ p14. A Protocol on the Use of Titanium Dioxide Chromatography/ \% x8 L- b$ v6 j, r
for Phosphoproteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
/ q% R$ i- C2 t2 R; H3 a# p2 pMartijn W.H. Pinkse, Simone Lemeer, and Albert J.R. Heck' C, U9 j/ n- j9 r; n$ x
15. Positional Proteomics at the N-Terminus as a Means of Proteome Simplification . 229) E3 V: z3 P/ c" `, H
Gemma R. Davidson, Stuart D. Armstrong, and Robert J. Beynon3 }) B5 z' f) V6 o" ^7 G# Z" C
16. N-Terminomics: A High-Content Screen for Protease Substrates
) z; Y( G3 q( t0 R* R( Band Their Cleavage Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243& q& G  _6 c+ s' `4 q% `8 t
John C. Timmer and Guy S. Salvesen) x+ a" _. s" e2 ?) n) r. }8 w  u
17. Protease Specificity Profiling by Tandem Mass Spectrometry Using
' P1 k) J2 W/ jProteome-Derived Peptide Libraries . . . . . . . . . . . . . . . . . . . . . . . . 257: D4 G  x8 c8 h3 Q" [
Oliver Schilling, Ulrich auf dem Keller, and Christopher M. Overall. m- a; p6 h5 Y+ D. q$ }2 ?1 O/ l! K
18. Identification of Proteolytic Products and Natural Protein N-Termini
% }3 X+ g/ _* U4 ?, r. X3 w9 Aby Terminal Amine Isotopic Labeling of Substrates (TAILS) . . . . . . . . . . . . 273  e  ]: x" S, y, h" M
Alain Doucet, Oded Kleifeld, Jayachandran N. Kizhakkedathu,1 b1 d6 Q7 @4 N5 Y8 P9 [
and Christopher M. Overall$ m8 ^# |( d( }# \  X
19. Lectins as Tools to Select for Glycosylated Proteins . . . . . . . . . . . . . . . . 289# t8 A) b* A9 F* I3 P5 L
Els J.M. Van Damme) r4 m0 S$ a, k) c7 _
20. Strong Cation Exchange Chromatography for Analysis of Sialylated Glycopeptides 299- ?9 @" W0 m/ @9 G, {
Katharina Lohrig, Albert Sickmann, and Urs Lewandrowski
/ a2 D! U; z" @21. Titanium Dioxide Enrichment of Sialic Acid-Containing Glycopeptides . . . . . . 309: x. a6 F$ C: N' A* C
Giuseppe Palmisano, Sara E. Lendal, and Martin R. Larsen* e! \/ O3 K6 Z. _
22. Chemical De-O-glycosylation of Glycoproteins for Applications
3 }" T, b- |* }" V  e" Z5 Vin LC-Based Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
" ~( A: i- t( ^7 M! E! u; @Franz-Georg Hanisch6 j/ K$ T9 S3 c/ E7 v
23. Ubiquitination and Degradation of Proteins . . . . . . . . . . . . . . . . . . . . 335) _, r2 |7 B- ^  z: o
Yelena Kravtsova-Ivantsiv and Aaron Ciechanover3 @% V& Q  C5 e+ h" C# U
24. Bioinformatics Challenges in Mass Spectrometry-Driven Proteomics . . . . . . . 359+ Y5 K1 x8 {' M: g7 t+ h
Lennart Martens
5 k: o. p" S  p) X8 T6 s6 t# T25. A Case Study on the Comparison of Different Software Tools/ p5 U4 C+ U& @5 B7 s8 w
for Automated Quantification of Peptides . . . . . . . . . . . . . . . . . . . . . 3737 I" Q) }- [; q, W% ?
Niklaas Colaert, Joël Vandekerckhove, Lennart Martens,
3 c/ t" J) B/ ?+ r' g  C4 i! v0 `and Kris Gevaert. j' M. O. i) y4 K7 C+ Q/ ~# ]9 W
Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399; V# w- U# ]& s( b* q
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