Urinary Proteome Profiling Using 2D-DIGE and LC-MS/MS - LC-MS/MS in Proteomics: Methods and Applications - page 305

water can
improve visualisation of low-abundance proteins.
(16) CCB staining is required as minimal labelling does not
define the spot centre where concentration is highest.
Defining this centre improves protein identification suc-
cess rate from in gel tryptic digests of 2D-DIGE gel spots.

washing for several hours in Milli-Q 18

References

1. Pastwa, E., Somiari, S. B., Czyz, M., and
Somiari, R. I. (2007) Proteomics in human
cancer research. Proteom. Clin. Appl. 1 (1),
4-17.
2. Jemal, A., et al. (2007) Cancer statistics,
2007. CA Cancer J. Clin . 57 (1), 43-66.
3. Weeks, M. E., Hariharan, D., Petronije-
vic, L., Radon, T. P., Whiteman, H. J.,
Kocher, H. M., Timms, J. F., Lemoine, N.
R.,Crnogorac-Jurcevic, T. (2008) Analysis of
the urine proteome in patients with pancre-
atic ductal adenocarcinoma. Proteom. Clin.
Appl. 2 (7-8), 1047-1057.
4. Pieper, R., et al. (2004) Characterization of
the human urinary proteome: a method for
high-resolution display of urinary proteins on
two-dimensional electrophoresis gels with a
yield of nearly 1400 distinct protein spots.
Proteomics 4 (4), 1159-1174.
5. Spahr, C. S., et al. (2001) Towards defin-
ing the urinary proteome using liquid
chromatography-tandem mass spectrometry.
I. Profiling an unfractionated tryptic digest.
Proteomics 1 (1), 93-107.
6. Adachi, J., Kumar, C., Zhang, Y., Olsen, J.
V., and Mann, M. (2006) The human uri-
nary proteome contains more than 1500 pro-
teins, including a large proportion of mem-
brane proteins. Genome Biol. 7 (9), R80.
7. Barratt, J. and Topham, P. (2007) Urine pro-
teomics: the present and future of measur-
ing urinary protein components in disease.
CMAJ. 177 (4), 361-368.
8. Thongboonkerd, V. (2005) Genomics, pro-
teomics and integrative “omics” in hyperten-
sion research. Curr. Opin. Nephrol. Hyper-
tens. 14 (2), 133-139.
9. Comte, B., et al. (2006) Detection of bile
salt-dependent lipase, a 110 kDa pancreatic
protein, in urines of healthy subjects. Kidney
Int. 69 (6), 1048-1055.
10. Schaub, S., et al. (2004) Urine pro-
tein profiling with surface-enhanced laser-
desorption/ionization time-of-flight mass
spectrometry. Kidney Int. 65 (1), 323-332.
11. O'Farrell PH (1975) High resolution two-
dimensional electrophoresis of proteins. J.
Biol. Chem. 250 (10), 4007-4021.

12. Unlu, M., Morgan, M. E., and Minden,
J. S. (1997) Difference gel electrophoresis:
a single gel method for detecting changes
in protein extracts. Electrophoresis 18 (11),
2071-2077.
13. Marouga, R., David, S., and Hawkins, E.
(2005) The development of the DIGE sys-
tem: 2D fluorescence difference gel analy-
sis technology. Anal. Bioanal. Chem . 382 (3),
669-678.
14. Tonge, R., et al. (2001) Validation and devel-
opment of fluorescence two-dimensional dif-
ferential gel electrophoresis proteomics tech-
nology. Proteomics 1 (3), 377-396.
15. DeSouza, L., et al. (2005) Search for can-
cer markers from endometrial tissues using
differentially labeled tags iTRAQ and cICAT
with multidimensional liquid chromatogra-
phy and tandem mass spectrometry. J. Pro-
teome Res . 4 (2), 377-386.
16. Yin, H., Killeen, K., Brennen, R., Sobek,
D., Werlich, M., and van de Goor, T.
(2005) Microfluidic chip for peptide anal-
ysis with an integrated HPLC column,
sample

enrichment column, and nano-

electrospray tip. Anal. Chem . 77 (2),

527-533.
17. Chan, H. L., et al. (2005) Proteomic
analysis of redox- and ErbB2-dependent
changes in mammary luminal epithelial cells
using cysteine- and lysine-labelling two-
dimensional difference gel electrophoresis.
Proteomics 5 (11), 2908-2926.
18. Gharbi, S., et al. (2002) Evaluation of two-
dimensional differential gel electrophoresis
for proteomic expression analysis of a model
breast cancer cell system. Mol. Cell Proteomics
1 (2), 91-98.
19. Weeks, M. E., et al. (2006) A paral-

lel proteomic and metabolomic analysis

of the hydrogen peroxide- and Sty1p-

dependent stress response in Schizosac-

charomyces pombe. Proteomics 6 (9),

2772-2796.
20. Shaw, M. M. and Riederer, B. M. (2003)
Sample preparation for two-dimensional

gel electrophoresis. Proteomics 3 (8),

1408-1417.