Biology Reference
In-Depth Information
and phosphorylations on serine and threonine. They are
commonly used as a complement to CID or HCD
spectra.
(d) Data analysis. Mascot is the most common but not the
only search engine that can be used for viral proteome
analysis. Alternative engines are for example SEQUEST
and X!Tandem. The general rule is that no search engine
works properly if more than six variable modifi cations are
set. Consequently, to search for more than four PTMs, it
is necessary to perform several consecutive searches using
different sets of variable PTMs.
Acknowledgement
This work was supported by the P.O. Zetterling Foundation (SBL),
the Swedish Cancer Society (SBL), and the Kjell and Märta Beijer
Foundation (UP). The authors wish to thank Lioudmila Elfi neh
for valuable discussions.
References
1. Flint SJ (2001) Adenovirus. Encyclopedia of
life sciences. Wiley.
http://www.els.net
2. Russell WC (2000) Update on adenovirus and
its vectors. J Gen Virol 81:2573-2604
3. Stewart PL, Fuller SD, Burnett RM (1993)
Difference imaging of adenovirus: bridging the
resolution gap between X-ray crystallography
and electron microscopy. EMBO J 12:
2589-2599
4. van Oostrum J, Burnett RM (1985) Molecular
composition of the adenovirus type 2 virion.
J Virol 56:439-448
5. Fuschiotti P, Schoehn G, Fender P, Fabry CM,
Hewat EA, Chroboczek J et al (2006) Structure
of the dodecahedral penton particle from human
adenovirus type 3. J Mol Biol 356:510-520
6. Rux JJ, Kuser PR, Burnett RM (2003)
Structural and phylogenetic analysis of adeno-
virus hexons by use of high-resolution x-ray
crystallographic, molecular modeling, and
sequence-based methods. J Virol 77:
9553-9566
7. Zubieta C, Schoehn G, Chroboczek J, Cusack
S (2005) The structure of the human adenovi-
rus 2 penton. Mol Cell 17:121-135
8. Liu H, Jin L, Koh SB, Atanasov I, Schein S, Wu
L et al (2010) Atomic structure of human ade-
novirus by cryo-EM reveals interactions among
protein networks. Science 329:1038-1043
9. Reddy VS, Natchiar SK, Stewart PL, Nemerow
GR (2010) Crystal structure of human
adenovirus at 3.5 A resolution. Science 329:
1071-1075
10. Washburn MP, Wolters D, Yates JR 3rd (2001)
Large-scale analysis of the yeast proteome by
multidimensional protein identifi cation tech-
nology. Nat Biotechnol 19:242-247
11. Johnson RS, Davis MT, Taylor JA, Patterson
SD (2005) Informatics for protein identifi ca-
tion by mass spectrometry. Methods 35:
223-236
12. Jensen ON (2006) Interpreting the protein
language using proteomics. Nat Rev Mol Cell
Biol 7:391-403
13. Thingholm TE, Jensen ON, Larsen MR (2009)
Analytical strategies for phosphoproteomics.
Proteomics 9:1451-1468
14. Bodenmiller B, Mueller LN, Mueller M,
Domon B, Aebersold R (2007) Reproducible
isolation of distinct, overlapping segments of
the phosphoproteome. Nat Methods 4:
231-237
15. Wisniewski JR, Zougman A, Kruger S, Mann
M (2007) Mass spectrometric mapping of
linker histone H1 variants reveals multiple acet-
ylations, methylations, and phosphorylation as
well as differences between cell culture and
tissue. Mol Cell Proteomics 6:72-87
16. Bergstrom Lind S, Artemenko KA, Elfi neh L,
Zhao Y, Bergquist J, Pettersson U (2012) The
phosphoproteome of the adenovirus type 2
virion. Virology 433:253-261
