Biomedical Engineering Reference
In-Depth Information
19. Friedman, D.B., Stauff, D.L., Pishchany, G.
et al
. (2006)
Staphylococcus aureus
redirects central
metabolism to increase iron availability.
PLoS Pathogens
,
2
(8), e87.
20. Friedman, D.B., Wang, S.E., Whitwell, C.W.
et al
. (2007) Multivariable difference gel elec-
trophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2
signaling.
Molecular & Cellular Proteomics
,
6
, 150-169. DIGE experimental design.
21. Seike, M., Kondo, T., Fujii, K.
et al
. (2004) Proteomic signature of human cancer cells.
Pro-
teomics
,
4
(9), 2776-2788. DIGE experimental design.
22. Suehara, Y., Kondo, T., Fujii, K.
et al
. (2006) Proteomic signatures corresponding to histolog-
ical classification and grading of soft-tissue sarcomas.
Proteomics
,
6
(15), 4402-4409. DIGE
experimental design.
23. Karp, N.A. and Lilley, K.S. (2005) Maximising sensitivity for detecting changes in protein expres-
sion: experimental design using minimal CyDyes.
Proteomics
,
5
(12), 3105-3115. Variation in
proteomics experiments, and statistical power for DIGE experiments.
24. Alban, A., David, S.O., Bjorkesten, L.
et al
. (2003) A novel experimental design for compara-
tive two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a
pooled internal standard.
Proteomics
,
3
(1), 36-44. First description of internal standard method-
ology for DIGE.
25. Friedman, D.B., Hill, S., Keller, J.W.
et al
. (2004) Proteome analysis of human colon cancer
by two-dimensional difference gel electrophoresis and mass spectrometry.
Proteomics
,
4
(3),
793-811. DIGE internal standard and limit of sensitivity.
26. Hatakeyama, H., Kondo, T., Fujii, K.
et al
. (2006) Protein clusters associated with carcinogen-
esis, histological differentiation and nodal metastasis in esophageal cancer.
Proteomics
,
6
(23),
6300-6316.
27. Kolkman, A., Dirksen, E.H., Slijper, M. and Heck, A.J. (2005) Double standards in quantitative
proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable
isotope labeling.
Molecular & Cellular Proteomics
,
4
(3), 255-266 [Epub 2005 Jan 4].
28. Wu, C.C., Yates, J.R. III, Neville, M.C. and Howell, K.E. (2000) Proteomic analysis of two
functional states of the Golgi complex in mammary epithelial cells.
Traffic
,
1
(10), 769-782.
29. Ohi, M.D., Link, A.J., Ren, L.
et al
. (2002) Proteomics analysis reveals stable multiprotein com-
plexes in both fission and budding yeasts containing Myb-related Cdc5p/Cef1p, novel pre-mRNA
splicing factors, and snRNAs.
Molecular and Cellular Biology
,
22
(7), 2011-2024.
30. Sanders, S.L., Jennings, J., Canutescu, A.
et al
. (2002) Proteomics of the eukaryotic transcription
machinery: identification of proteins associated with components of yeast TFIID by multidimen-
sional mass spectrometry.
Molecular and Cellular Biology
,
22
(13), 4723-4738.
31. Washburn, M.P., Wolters, D. and Yates, J.R. III (2001) Large-scale analysis of the yeast proteome
by multidimensional protein identification technology.
Nature Biotechnology
,
19
(3), 242-247.
MudPIT analysis.
32. Florens, L., Washburn, M.P., Raine, J.D.
et al
. (2002) A proteomic view of the
Plasmodium
falciparum
life cycle.
Nature
,
419
(6906), 520-526.
33. Gygi, S.P., Rist, B., Gerber, S.A.
et al
. (1999) Quantitative analysis of complex protein mixtures
using isotope-coded affinity tags.
Nature Biotechnology
,
17
(10), 994-999. ICAT labeling for
quantitative LC/MS/MS.
34. Ross, P.L., Huang, Y.N., Marchese, J.N.
et al
. (2004) Multiplexed protein quantitation in
Sac-
charomyces cerevisiae
using amine-reactive isobaric tagging reagents.
Molecular & Cellular
Proteomics
,
3
(12), 1154-1169 [Epub 2004 Sep 22]. iTRAQ labeling for quantitative LC/MS/MS.