PDF电子书：Gel-Free Proteomics

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. c$ L' E% U) c8 NGel-Free Proteomics: t: m& Q7 @% H. t3 ~2 D
Contents
8 x! e* ]3 Q8 q5 O8 [, ~Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v" p1 T- |% _1 H* I; a
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
/ F% R, W( }( W" a1 s3 }1. Mass Spectrometry-Driven Proteomics: An Introduction . . . . . . . . . . . . . 1. z1 D+ ~, W% {$ _* y
Kenny Helsens, Lennart Martens, Joël Vandekerckhove,% j) h! I! g/ @8 e- v, V
and Kris Gevaert
" z7 G2 r/ g5 G, M& @9 P1 m2. Metabolic Labeling of Model Organisms Using Heavy Nitrogen (15N) . . . . . . 29' ]& X6 F/ q. ?) S5 `
Joost W. Gouw, Bastiaan B.J. Tops, and Jeroen Krijgsveld
- r/ @; C8 R: z2 Q3. Trypsin-Catalyzed Oxygen-18 Labeling for Quantitative Proteomics . . . . . . . 43
, j- ]0 R) }5 F! U9 D1 J8 O4 pWei-Jun Qian, Brianne O. Petritis, Carrie D. Nicora,
6 B; d: n% n" X8 N7 U8 j9 Tand Richard D. Smith
) s% J. W8 B" v9 \3 {4. ICPL Labeling Strategies for Proteome Research . . . . . . . . . . . . . . . . . 55
0 \/ Q, _& E4 ~Friedrich Lottspeich and Josef Kellermann
& _: _/ C* w! i" i, ?5. Quantitative Proteome Analysis Using Isobaric Peptide Termini: V3 i. ~6 }6 l1 T1 c0 x( T
Labeling (IPTL) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
' G8 s! z: G. ]% NMagnus Ø. Arntzen, Christian J. Koehler, Achim Treumann, and Bernd Thiede
; d9 J% T1 S) p# o( B6 {6 F6. Complete Chemical Modification of Amine and Acid Functional Groups
4 N  H" Y# S" j+ H) {of Peptides and Small Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . 77$ o8 g. C8 f$ v  D: u  d
Casey J. Krusemark, Brian L. Frey, Lloyd M. Smith, and Peter J. Belshaw
/ z4 C7 E) N3 p1 t0 w7. Production and Use of Stable Isotope-Labeled Proteins for Absolute
, C( @9 D0 ~' p$ Z6 hQuantitative Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
! @6 f$ _* v4 E( WDorothée Lebert, Alain Dupuis, Jérôme Garin, Christophe Bruley,
5 i1 `0 X1 }/ X; U7 Nand Virginie Brun9 }, h2 U+ S+ m# a! C
8. Organelle Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
# Q) Z! \# t( m6 \! r( {; ySophie Duclos and Michel Desjardins
6 H. `" Q9 ~$ b8 g9. Membrane Protein Digestion – Comparison of LPI HexaLane/ Z- s# U1 |0 s8 D, o) @+ K) M
with Traditional Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
3 r& P  g" G0 Q1 B0 X' gPing Sui, Tasso Miliotis, Max Davidson, Roger Karlsson, and Anders Karlsson8 a* j* a4 S+ ]
10. GeLCMS for In-Depth Protein Characterization and Advanced Analysis
, J, [* n4 b" L/ K$ V. A+ j. X" Bof Proteomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
9 I4 Y, E  ?- V$ j* gAlicia Lundby and Jesper V. Olsen: B: C& W7 u5 y0 t( y
11. Exploring New Proteome Space: Combining Lys-N Proteolytic Digestion/ ~! Y$ Z; y3 @8 \  G0 ?9 I* R
and Strong Cation Exchange (SCX) Separation in Peptide-Centric! k0 v* [0 @$ }4 ^% Q
MS-Driven Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
$ Q. ~8 t6 e2 ]6 ?$ m12. Quantitation of Newly Synthesized Proteins by Pulse Labeling
  R2 |# H: Z4 ]. _, f4 qwith Azidohomoalanine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
& |# r4 B6 ]( R: lGertjan Kramer, Piotr T. Kasper, Luitzen de Jong, and Chris G. de Koster
3 z3 J! y; P. S* R( e+ Q( \13. Analytical Strategies in Mass Spectrometry-Based Phosphoproteomics . . . . . . . 1831 T6 P% p' X4 H6 \, k5 o4 k
Heidi Rosenqvist, Juanying Ye, and Ole N. Jensen
$ e% z6 ]0 K2 G3 c1 H14. A Protocol on the Use of Titanium Dioxide Chromatography' q1 T8 r- p1 g8 u7 z
for Phosphoproteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
* |1 t& @) P9 ZMartijn W.H. Pinkse, Simone Lemeer, and Albert J.R. Heck* g! Y+ {: s2 H. a% f+ J
15. Positional Proteomics at the N-Terminus as a Means of Proteome Simplification . 2290 ^: {; \2 D9 Z6 @$ V) c
Gemma R. Davidson, Stuart D. Armstrong, and Robert J. Beynon
+ M6 Y( F+ d& T! j/ _% J16. N-Terminomics: A High-Content Screen for Protease Substrates) [- n: q* J, q1 H
and Their Cleavage Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
3 @0 V3 L  V* f0 q% L. U3 h8 uJohn C. Timmer and Guy S. Salvesen
& P0 W, o# A! E. y# g" D( s17. Protease Specificity Profiling by Tandem Mass Spectrometry Using+ h8 @# r% N  B& c
Proteome-Derived Peptide Libraries . . . . . . . . . . . . . . . . . . . . . . . . 257
5 Y; X6 U( `9 F' f5 A, t4 ZOliver Schilling, Ulrich auf dem Keller, and Christopher M. Overall
4 M7 b; ?& a) y. d* u18. Identification of Proteolytic Products and Natural Protein N-Termini& _: R  ^, ?& L2 z/ \: P0 u# c
by Terminal Amine Isotopic Labeling of Substrates (TAILS) . . . . . . . . . . . . 273
8 Z( l: o7 H2 }/ \" u) ?9 hAlain Doucet, Oded Kleifeld, Jayachandran N. Kizhakkedathu,
' m" j+ w- S  Y- z% Z" Hand Christopher M. Overall
: E: q, w0 e* G+ Z# U19. Lectins as Tools to Select for Glycosylated Proteins . . . . . . . . . . . . . . . . 289
+ f  k% ?# _* C' h) j7 iEls J.M. Van Damme
0 Z! j" n: ?! U- o20. Strong Cation Exchange Chromatography for Analysis of Sialylated Glycopeptides 299. K" `: N: x6 {
Katharina Lohrig, Albert Sickmann, and Urs Lewandrowski
0 n- I: S* ^/ [21. Titanium Dioxide Enrichment of Sialic Acid-Containing Glycopeptides . . . . . . 309
" n; a1 Y8 _5 H( CGiuseppe Palmisano, Sara E. Lendal, and Martin R. Larsen
" n9 p$ ?. \9 d& s. E22. Chemical De-O-glycosylation of Glycoproteins for Applications
) }: v. m: w- B' P) E$ j  _in LC-Based Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3231 Q9 ]  W/ m8 o/ {1 ~
Franz-Georg Hanisch) D$ V6 L9 `$ ^+ F/ _
23. Ubiquitination and Degradation of Proteins . . . . . . . . . . . . . . . . . . . . 335( @/ a" V) x/ C3 Y% U! {' {
Yelena Kravtsova-Ivantsiv and Aaron Ciechanover8 G  {, b/ r5 z8 O3 K9 Z
24. Bioinformatics Challenges in Mass Spectrometry-Driven Proteomics . . . . . . . 3595 o- f2 @+ I! g4 ^) f# r( r2 H
Lennart Martens
5 a& ~7 W5 S, `( k( I* M* V25. A Case Study on the Comparison of Different Software Tools
+ a" a0 D, w8 f2 ~for Automated Quantification of Peptides . . . . . . . . . . . . . . . . . . . . . 373* d7 C- a0 d* O8 V! |6 u) j" h* `
Niklaas Colaert, Joël Vandekerckhove, Lennart Martens,( |# z7 \( g0 {+ y* k( R! Z
and Kris Gevaert, Y  f6 ]% P: H" d& ~
Subject Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
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