Jacob D. Jaffe

Assistant Director of Proteomics
7 Cambridge Center, Room 5025
Cambridge, MA 02142

Jacob Jaffe is the Assistant Director of the Proteomics Platform at the Broad Institute. Proteomics is the study of the full complement of proteins encoded in the human genome along with changes made to the proteins after they are created, known as post-translational modifications.

In the cell’s nucleus, DNA wraps around chromatin proteins called histones, which can carry a variety of post-translational modifications, often thought of as chromatin "marks." Dr. Jaffe’s primary research interest is the biochemistry of these histone marks, which are part of the cell’s "epigenome" — inherited genetic elements other than DNA. It has recently been shown that certain combinations of chromatin marks greatly influence the activity of DNA with which they are associated. Through techniques developed in the Proteomics Platform, Dr. Jaffe has been able to characterize a full complement of these marks. He aims to understand how chromatin marks change in models of cellular differentiation and disease, and explore the idea of epigenetic signatures that can differentiate among cancers.

As Assistant Director of the platform, Dr. Jaffe also directs research aimed at elucidating protein-protein, protein-DNA, and protein-small molecule interactions. The core enabling technology of Dr. Jaffe’s work is mass spectrometry, which allows precise identification and quantification of thousands of proteins in an unbiased manner. Jaffe is an expert in the quantitative analysis of the proteome using stable-isotope labeling techniques (such as SILAC or iTRAQ), as well as algorithmic development for statistical modeling of proteomics data.

Dr. Jaffe joined the Broad in 2004 after earning a Ph.D. in biology/biochemistry from Harvard University in the laboratories of Broad Senior Associate Member George Church and Howard Berg.

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Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD. Quantitative assessment of ChIP-grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol Cell Proteomics. 2012 Mar 23. [Epub ahead of print] PubMed PMID: 22442256.

Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D, Peach SE, Shanower G, Zheng H, Kuroda MI, Pirrotta V, Park PJ, Elgin SC, Karpen GH. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb;21(2):147-63. PubMed PMID: 21177972.

Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA. iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics. Mol Cell Proteomics. 2011 Dec 30. [Epub ahead of print] PubMed PMID: 22210691.

Markljung E, Jiang L, Jaffe JD, Mikkelsen TS, Wallerman O, Larhammar M, Zhang X, Wang L, Saenz-Vash V, Gnirke A, Lindroth AM, Barres R, Yan J, Stromberg S, De S, Ponten F, Lander ES, Carr SA, Zierath JR, Kullander K, Wadelius C, Lindblad-Toh K, Andersson G, Hjalm G, Andersson L. ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth. PLoS Biol. 2009 Dec;7(12):e1000256. Epub 2009 Dec 15. PubMed PMID: 20016685.

Rudomin EL, Carr SA, Jaffe JD. Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx). J Proteome Res. 2009 Jun;8(6):3154-60. PubMed PMID: 19344186.

Jaffe JD, Keshishian H, Chang B, Addona TA, Gillette MA, Carr SA. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification. Mol Cell Proteomics. 2008 Oct;7(10):1952-62. Epub 2008 Jun 4. PubMed PMID: 18534968.

Lindell D, Jaffe JD, Coleman ML, Futschik ME, Axmann IM, Rector T, Kettler G, Sullivan MB, Steen R, Hess WR, Church GM, Chisholm SW. Genome-wide expression dynamics of a marine virus and host reveal features of co-evolution. Nature. 2007 Sep 6;449(7158):83-6. PubMed PMID: 17805294.

Leptos KC, Sarracino DA, Jaffe JD, Krastins B, Church GM. MapQuant: open-source software for large-scale protein quantification. Proteomics. 2006 Mar;6(6):1770-82. PubMed PMID: 16470651.

Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics. 2004 Jan;4(1):59-77. PubMed PMID: 14730672.