Biology Reference
In-Depth Information
diversity in Caenorhabditis elegans and suggests an atypical
translocation mechanism for integral membrane proteins. Mol
Cell Proteomics 2007;6:2100
e
9.
[154] Zielinska DF, Gnad F, Wisniewski JR, Mann M. Precision
mapping of an in vivo N-glycoproteome reveals rigid topological
and sequence constraints. Cell 2010;141:897
e
907.
[155] Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D,
Marsischky G, et al. A proteomics approach to understanding
protein ubiquitination. Nat Biotechnol 2003;21:921
e
6.
[156] Xu G, Paige JS, Jaffrey SR. Global analysis of lysine ubiquiti-
nation by ubiquitin remnant immunoaffinity profiling. Nat Bio-
technol 2010;28:868
e
73.
[157] Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M,
et al. A proteome-wide, quantitative survey of in vivo ubiq-
uitylation sites reveals widespread regulatory roles. Mol Cell
Proteomics 2011;10:M111.013284.
[158] Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, et al.
Systematic and quantitative assessment of the ubiquitin-modified
proteome. Mol Cell 2011;44:325
e
40.
[159] Ong SE, Mittler G, Mann M. Identifying and quantifying in vivo
methylation sites by heavy methyl SILAC. Nat Methods 2004;1:
119
e
26.
[160] Zhao Y, Jensen ON. Modification-specific proteomics: strategies
for characterization of post-translational modifications using
enrichment techniques. Proteomics 2009;9:4632
[171] Lee JS, Smith E, Shilatifard A. The language of histone crosstalk.
Cell 2010;142:682
5.
[172] Wu SL, Kim J, Bandle RW, Liotta L, Petricoin E, Karger BL.
Dynamic profiling of the post-translational modifications and
interaction partners of epidermal growth factor receptor signaling
after stimulation by epidermal growth factor using Extended
Range Proteomic Analysis (ERPA). Mol Cell Proteomics 2006;5:
1610
e
27.
[173] Siuti N, Kelleher NL. Decoding protein modifications using top-
down mass spectrometry. Nature methods 2007;4:817
e
21.
[174] Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, et al.
PHOSIDA (phosphorylation site database): management, struc-
tural and evolutionary investigation, and prediction of phospho-
sites. Genome Biol 2007;8:R250.
[175] Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, et al. Lysine
acetylation is a highly abundant and evolutionarily conserved
modification
e
in Escherichia
coli. Mol Cell Proteomics
2009;8:215
e
25.
[176] Collins MO, Yu L, Campuzano I, Grant SGN, Choudhary JS.
Phosphoproteomic analysis of the mouse brain cytosol reveals
a predominance of protein phosphorylation in regions of intrinsic
sequence disorder. Mol Cell Proteomics 2008;7:1331
e
48.
[177] Villen J, Beausoleil SA, Gerber SA, Gygi SP. Large-scale phos-
phorylation analysis of mouse liver. Proc Natl Acad Sci U S A
2007;104:1488
41.
[161] Macek B, Mann M, Olsen JV. Global and site-specific quantitative
phosphoproteomics: principles and applications. Annual review of
pharmacology and toxicology 2009;49:199
93.
[178] Wisniewski JR, Nagaraj N, Zougman A, Gnad F, Mann M. Brain
phosphoproteome obtained by a FASP-based method reveals
plasma membrane protein topology. J Proteome Res 2010;9:
3280
e
9.
[179] Monetti M, Nagaraj N, Sharma K, Mann M. Large-scale phos-
phosite quantification in tissues by a spike-in SILAC method. Nat
Methods 2011;8(8):655
e
8.
[180] Liu H, Sadygov RG, Yates 3rd JR. A model for random sampling
and estimation of relative protein abundance in shotgun proteo-
mics. Anal Chem 2004;76:4193
e
201.
[181] Gao J, Opiteck GJ, Friedrichs MS, Dongre AR, Hefta SA.
Changes in the protein expression of yeast as a function of carbon
source. J Proteome Res 2003;2:643
e
9.
[182] Mann M. Functional and quantitative proteomics using SILAC.
Nat Rev Mol Cell Biol 2006;7:952
e
8.
[183] Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J,
Schmidt G, et al. Tandem mass tags: a novel quantification
strategy for comparative analysis of complex protein mixtures by
MS/MS. Anal Chem 2003;75:1895
e
904.
[184] Ross PL, Huang YN, Marchese JN, Williamson B, Parker K,
Hattan S, et al. Multiplexed protein quantitation in Saccharo-
myces cerevisiae using amine-reactive isobaric tagging reagents.
Mol Cell Proteomics 2004;3:1154
e
69.
[185] Hsu JL, Huang SY, Chow NH, Chen SH. Stable-isotope dimethyl
labeling for quantitative proteomics. Anal Chem 2003;75:
6843
e
e
221.
[162] Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM.
Multiple reaction monitoring for robust quantitative proteomic
analysis of cellular signaling networks. Proc Natl Acad Sci U S A
2007;104:5860
e
5.
[163] Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT,
Ericson C, et al. Profiling of tyrosine phosphorylation pathways in
human cells using mass spectrometry. Proc Natl Acad Sci U S A
2003;100:443
e
8.
[164] Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis
of phosphotyrosine-dependent signaling networks by quantitative
proteomics. Nat Biotechnol 2004;22:1139
e
45.
[165] Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML,
Jensen LJ, et al. Quantitative phosphoproteomics reveals wide-
spread full phosphorylation site occupancy during mitosis. Sci
Signal 2010;3:ra3.
[166] Wu RH, Haas W, Dephoure N, Huttlin EL, Zhai B, Sowa ME,
et al. A large-scale method to measure absolute protein phos-
phorylation stoichiometries. Nat Methods 2011;8:677
e
83.
[167] Bishop AC, Buzko O, Shokat KM. Magic bullets for protein
kinases. Trends in Cell Biology 2001;11:167
e
72.
[168] Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D,
Pedrioli PG, et al. Phosphoproteomic analysis reveals inter-
connected system-wide responses to perturbations of kinases and
phosphatases in yeast. Sci Signal 2010;3(153). rs4.
[169] Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V,
Larsen B, et al. A global protein kinase and phosphatase inter-
action network in yeast. Science 2010;328:1043
e
6.
[170] Hunter T. The age of crosstalk: phosphorylation, ubiquitination,
and beyond. Molecular Cell 2007;28:730
e
8.
e
52.
[186] Boersema PJ, Raijmakers R, Lemeer S, Mohammed S, Heck AJ.
Multiplex peptide stable isotope dimethyl labeling for quantitative
proteomics. Nat Protoc 2009;4:484
e
94.
[187] Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J,
et al. A database of mass spectrometric assays for the yeast pro-
teome. Nat Methods 2008;5:913
e
4.
e
