Unbiased identification of protein-bait interactions using biochemical enrichment and quantitative proteomicsShao En Ong
The Broad Institute of MIT and Harvard, Cambridge MA 02142, USA
Cold Spring Harb Protoc 2010:pdb.prot5400. 2010
..The combination of biochemical enrichment and quantitative proteomics allows rapid characterization of molecular baits with their interacting proteins, providing tremendous insight into their biological mechanisms of action...
- Identifying cellular targets of small-molecule probes and drugs with biochemical enrichment and SILAC
Shao En Ong
Proteomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
Methods Mol Biol 803:129-40. 2012
..We describe the use of SILAC in identifying proteins that bind small-molecule probes and drugs in a cellular context...
Whole proteomes as internal standards in quantitative proteomicsShao En Ong
Proteomics and Biomarker Discovery Platform, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Genome Med 2:49. 2010
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- DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization
H Christian Reinhardt
David H Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02132, USA
Mol Cell 40:34-49. 2010
..Our findings demonstrate a critical role for the MK2 pathway in the posttranscriptional regulation of gene expression as part of the DNA damage response in cancer cells...
- Empirical Bayes analysis of quantitative proteomics experiments
Adam A Margolin
Cancer Program, The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
PLoS ONE 4:e7454. 2009
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- iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics
Philipp Mertins
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Mol Cell Proteomics 11:M111.014423. 2012
..Spike-in experiments using peptides of defined ratios in a background of nonregulated peptides show that iTRAQ quantification is less accurate but not as variable as mTRAQ quantification...
- Identifying the proteins to which small-molecule probes and drugs bind in cells
Shao En Ong
Proteomics Platform, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Proc Natl Acad Sci U S A 106:4617-22. 2009
..Here, we describe in full detail the application of the method to identify targets of kinase inhibitors and immunophilin binders...
- AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics
Letian Kuai
Stanley Center for Psychiatric Research, 7 Cambridge Center, Cambridge, MA 02142, USA
Chem Biol 18:891-906. 2011
..Similar strategies should lead to the discovery of novel targets for therapeutic development...
- Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach
Mark N Lee
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Immunol 14:179-85. 2013
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- A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint
Marcel A T M van Vugt
David H Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
PLoS Biol 8:e1000287. 2010
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Stable isotope labeling by amino acids in cell culture for quantitative proteomicsShao En Ong
Proteomics and Biomarker Discovery, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
Methods Mol Biol 359:37-52. 2007
..In this chapter, we provide detailed SILAC protocols and explain how to incorporate SILAC into any experiment...
- A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC)
Shao En Ong
The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
Nat Protoc 1:2650-60. 2006
..This procedure can be completed in 8 days...
- Mass spectrometry-based proteomics turns quantitative
Shao En Ong
The Broad Institute of MIT and Harvard, 320 Bent Street, Cambridge, Massachusetts 02141, USA
Nat Chem Biol 1:252-62. 2005
..This isotopic handle facilitates direct quantification from the mass spectra. Using these quantitative approaches, precise functional information as well as temporal changes in the proteome can be captured by MS...
- Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate
Drew M Lowery
Department of Biology, Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
EMBO J 26:2262-73. 2007
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- CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis
Hui Liu
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 108:1379-84. 2011
..In addition, the Y734F mutation also eliminated enhanced Src activation. Thus, this work provides molecular mechanisms for the metastasis-enhancing functions of CDCP1...
