Biology Reference
In-Depth Information
9. Dried or reconstituted peptides can be stored at −80 °C for as
long as required.
10. nanoLC columns can also be purchased from suppliers such as
Michrom or New Objective.
11. It is not required to completely eliminate carryover between
injections as all the samples in a given set will be combined for
subsequent analysis.
12. Our experimental design consists of 16 SDS-PAGE gel slices
from each of the three biological replicates of a given sample.
This can be completed in 2½ days of mass spectrometric analy-
sis time.
13. We use the “mudpit combine” option in GPM searches to pro-
duce a unifi ed output fi le from the individual search result fi les.
Acknowledgements
KAN, ISG, and SM acknowledge support in the form of iMQRES
awards. SJE acknowledges support in the form of an APA scholar-
ship. PAH acknowledges funding support from the Australian
Research Council and wishes to thank Gayani Gammulla for pro-
viding images.
References
1. Weinberger KM, Easdown WJ, Yang R et al
(2009) Food crisis in the Asia-Pacifi c region.
Asia Pac J Clin Nutr 18:507-515
2. Goff SA, Ricke D, Lan TH et al (2002) A draft
sequence of the rice genome (Oryza sativa L.
ssp. japonica). Science 296:92-100
3. Rabbani MA, Maruyama K, Abe H et al (2003)
Monitoring expression profi les of rice genes
under cold, drought, and high-salinity stresses
and abscisic acid application using cDNA
microarray and RNA gel-blot analyses. Plant
Physiol 133:1755-1767
4. Koller A, Washburn MP, Lange B et al (2002)
Proteomic survey of metabolic pathways in
rice. Proc Natl Acad Sci U S A 99:
11969-11974
5. Link AJ, Eng J, Schieltz DM et al (1999)
Direct analysis of protein complexes using mass
spectrometry. Nat Biotechnol 17:676-682
6. Washburn MP, Wolters D, Yates JR (2001)
Large-scale analysis of the yeast proteome by
multidimensional protein identifi cation tech-
nology. Nat Biotechnol 19:242-247
7. Wolters DA, Washburn MP, Yates JR 3rd
(2001) An automated multidimensional
protein identifi cation technology for shotgun
proteomics. Anal Chem 73:5683-5690
8. Helmy M, Tomita M, Ishihama Y (2011)
OryzaPG-DB: rice proteome database based
on shotgun proteogenomics. BMC Plant Biol
11:63
9. Liu L, Bai L, Luo C et al (2011) Systematic
annotation and bioinformatics analyses of
large-scale Oryza sativa proteome. Curr Protein
Pept Sci 12:621-630
10. Nakagami H, Sugiyama N, Mochida K et al
(2010) Large-scale comparative phosphopro-
teomics identifi es conserved phosphorylation
sites in plants. Plant Physiol 153:1161-1174
11. Ong SE, Foster LJ, Mann M (2003) Mass
spectrometric-based approaches in quantitative
proteomics. Methods 29:124-130
12. Ong SE, Mann M (2005) Mass spectrometry-
based proteomics turns quantitative. Nat Chem
Biol 1:252-262
13. Steen H, Pandey A (2002) Proteomics goes
quantitative: measuring protein abundance.
Trends Biotechnol 20:361-364
14. Agrawal GK, Rakwal R (2011) Rice pro-
teomics: a move toward expanded proteome
