Biology Reference
In-Depth Information
a
bench-top Orbitrap. Mol Cell
Proteomics
2012;11:
purification procedure for interaction proteomics in mammalian
cells. Nat Methods 2006;3:1013
M111.013722.
[84] Geiger T, Wehner A, Schaab C, Cox J, Mann M. Comparative
proteomic analysis of eleven common cell lines reveals ubiquitous
but varying expression of most proteins. Mol Cell Proteomics
2012;11:M111.014050.
[85] Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J,
et al. Defining the transcriptome and proteome in three func-
tionally different human cell lines. Mol Syst Biol 2010;6:450.
[86] Malmstrom J, Beck M, Schmidt A, Lange V, Deutsch EW,
Aebersold R. Proteome-wide cellular protein concentrations of
the
9.
[101] Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, Bauer A,
et al. Functional organization of the yeast proteome by systematic
analysis of protein complexes. Nature 2002;415:141
e
7.
[102] Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL,
et al. Systematic identification of protein complexes in Saccha-
romyces cerevisiae by mass spectrometry. Nature 2002;415:
180
e
3.
[103] Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M,
et al. Proteome survey reveals modularity of the yeast cell
machinery. Nature 2006;440:631
e
6.
[104] Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A,
et al. Global landscape of protein complexes in the yeast
Saccharomyces cerevisiae. Nature 2006;440:637
e
43.
[105] Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR,
et al. A comprehensive analysis of protein
e
protein interactions in
Saccharomyces cerevisiae. Nature 2000;403:623
e
7.
[106] Ito T, Chiba T, Ozawa R, Yoshida M, Hattori M, Sakaki Y. A
comprehensive two-hybrid analysis to explore the yeast protein
interactome. Proc Natl Acad Sci U S A 2001;98:4569
e
74.
[107] Bader GD, Hogue CW. Analyzing yeast protein
e
protein inter-
action data obtained from different sources. Nat Biotechnol
2002;20:991
e
human
pathogen
Leptospira
interrogans.
Nature
2009;460:762
e
5.
[87] Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M. A protein
epitope signature Tag (PrEST) library allows SILAC-based
absolute quantification and multiplexed determination of protein
copy numbers in cell
lines. Mol Cell Proteomics 2012;11:
O111.009613.
[88] Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R,
Rajewsky N. Widespread changes in protein synthesis induced by
microRNAs. Nature 2008;455:58
e
63.
[89] Baek D, Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP. The
impact of microRNAs on protein output. Nature 2008;455:64
e
71.
[90] Bonaldi T, Straub T, Cox J, Kumar C, Becker PB, Mann M.
Combined use of RNAi and quantitative proteomics to study gene
function in Drosophila. Mol Cell 2008;31:762
7.
[108] Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K,
Sahalie J, et al. High-quality binary protein interaction map of the
yeast interactome network. Science 2008;322:104
e
72.
[91] Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J,
Wolf J, et al. Global quantification of mammalian gene expression
control. Nature 2011;473:337
e
42.
[92] Andersen JS, Lam YW, Leung AK, Ong SE, Lyon CE,
Lamond AI, et al. Nucleolar proteome dynamics. Nature
2005;433:77
e
83.
[93] Boisvert FM, Lam YW, Lamont D, Lamond AI. A quantitative
proteomics analysis of subcellular proteome localization and
changes induced by DNA damage. Mol Cell Proteomics
2010;9:457
e
70.
[94] Boisvert FM, Ahmad Y, Gierlinski M, Charriere F, Lamont D,
Scott M, et al. A quantitative spatial proteomics analysis of pro-
teome turnover in human cells. Mol Cell Proteomics 2010;
9:457
e
70.
[95] Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI.
Systematic analysis of protein pools, isoforms and modifications
affecting turnover and subcellular localisation. Mol Cell Proteo-
mics 2012;11:M111.013680.
[96] Stumpf MP, Thorne T, de Silva E, Stewart R, An HJ, Lappe M,
et al. Estimating the size of the human interactome. Proc Natl
Acad Sci U S A 2008;105:6959
e
64.
[97] Smith GP. Filamentous fusion phage: novel expression vectors
that display cloned antigens on the virion surface. Science
1985;228:1315
e
10.
[109] Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ,
Mann M. A proteomics strategy to elucidate functional protein
e
protein interactions applied to EGF signaling. Nat Biotechnol
2003;21:315
e
8.
[110] Ranish JA, Yi EC, Leslie DM, Purvine SO, Goodlett DR, Eng J,
et al. The study of macromolecular complexes by quantitative
proteomics. Nat Genet 2003;33:349
e
55.
[111] Schulze WX, Mann M. A novel proteomic screen for peptide
e
protein interactions. J Biol Chem 2004;279:10756
e
64.
[112] Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van
Schaik FM, Varier RA, et al. Selective anchoring of TFIID to
nucleosomes by trimethylation of histone H3 lysine 4. Cell
2007;131:58
e
69.
[113] Schulze WX, Deng L, Mann M. Phosphotyrosine interactome of
the ErbB-receptor kinase family. Mol Syst Biol 2005;1:
2005.0008.
[114] Hanke S, Mann M. The phosphotyrosine interactome of the
insulin receptor family and its substrates IRS-1 and IRS-2. Mol
Cell Proteomics 2009;8:519
e
34.
[115] Mittler G, Butter F, Mann M. A SILAC-based DNA protein
interaction screen that identifies candidate binding proteins to
functional DNA elements. Genome Res 2009;19:284
e
93.
[116] Butter F, Scheibe M, Morl M, Mann M. Unbiased RNA-protein
interaction screen by quantitative proteomics. Proc Natl Acad Sci
U S A 2009;106:10626
e
7.
[98] Fields S, Song O. A novel genetic system to detect protein
e
e
6.
[99] Rigaut G, Shevchenko A, Rutz B, Wilm M, Mann M, Seraphin B.
A generic protein purification method for protein complex char-
acterization
protein interactions. Nature 1989;340:245
31.
[117] Markljung E, Jiang L, Jaffe JD, Mikkelsen TS, Wallerman O,
Larhammar M, et al. ZBED6, a novel transcription factor derived
from a domesticated DNA transposon regulates IGF2 expression
and muscle growth. PLoS Biol 2009;7:e1000256.
[118] Butter F, Kappei D, Buchholz F, Vermeulen M, Mann M. A dom-
esticated transposon mediates the effects of a single-nucleotide
e
e
and
proteome
exploration. Nat Biotechnol
1999;17:1030
e
2.
[100] Burckstummer T, Bennett KL, Preradovic A, Schutze G,
Hantschel O, Superti-Furga G, et al. An efficient tandem affinity
