Overview. The proteomics core provides cutting-edge proteomics capabilities to the Center, ISB and many collaborators locally and worldwide. Recent accomplishments include: development of analytical and computational tools enabling comprehensive and systematic analysis of proteomes, subproteomes, and post translational modifications; development of software suites for evaluation and validation of proteomic datasets; and the design and implementation of targeted quantitative mass spectrometry (MS) experiments to analyze proteomes and subcellular proteomes. The core equipped with state-of-the-art MS technologies (see Resources) and will continue to disseminate and promote tools for high quality quantitative data acquisition and rapid implementation of new technologies. The core provides training and assistance on MS operation and experimental design, and assists with the Proteomics Informatics course (See Education and Training). Because the core is so integral to Center research, we provide below a description of ongoing technology development. Quantitative Proteomics. The core is a world leader in the development and application of both label and label-free quantitative proteomics for expression profiling and analysis of macromolecular assemblages. For example, the core, in collaboration with the Aitchison group, developed a novel automated approach to quantify peptides in SILAC experiments (QTIPs) along with new approaches for isolation of macromolecular complexes. These approaches significantly improved the identification of in vivo relevant interactions and led to extensive definition of signaling networks involved in peroxisome induction.
| Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona et al. (2018) Integrative structure and functional anatomy of a nuclear pore complex. Nature 555:475-482 |
| Kearney, Paul; Boniface, J Jay; Price, Nathan D et al. (2018) The building blocks of successful translation of proteomics to the clinic. Curr Opin Biotechnol 51:123-129 |
| Lee, Joon-Yong; Choi, Hyungwon; Colangelo, Christopher M et al. (2018) ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data. J Biomol Tech 29:39-45 |
| Tuttle, Lisa M; Pacheco, Derek; Warfield, Linda et al. (2018) Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Rep 22:3251-3264 |
| Maixner, Frank; Turaev, Dmitrij; Cazenave-Gassiot, Amaury et al. (2018) The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals. Curr Biol 28:2348-2355.e9 |
| Holden, Jennifer M; Koreny, Ludek; Obado, Samson et al. (2018) Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes. Mol Biol Cell 29:1100-1110 |
| Hoopmann, Michael R; Winget, Jason M; Mendoza, Luis et al. (2018) StPeter: Seamless Label-Free Quantification with the Trans-Proteomic Pipeline. J Proteome Res 17:1314-1320 |
| Slama, Patrick; Hoopmann, Michael R; Moritz, Robert L et al. (2018) Robust determination of differential abundance in shotgun proteomics using nonparametric statistics. Mol Omics 14:424-436 |
| Jabbari, Neda; Glusman, Gustavo; Joesch-Cohen, Lena M et al. (2018) Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1. PLoS One 13:e0198135 |
| Trachana, Kalliopi; Bargaje, Rhishikesh; Glusman, Gustavo et al. (2018) Taking Systems Medicine to Heart. Circ Res 122:1276-1289 |
Showing the most recent 10 out of 346 publications
