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Chick, Joel M.

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Chick

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Joel M.

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Chick, Joel M.

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2015 - 20162

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Author's Publications: search.filters.isAuthorOfPublication.b528394d-7b08-4ef5-b177-3708fee23d4a

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    An ultra-tolerant database search reveals that a myriad of modified peptides contributes to unassigned spectra in shotgun proteomics
    (2015) Chick, Joel M.; Kolippakkam, Deepak; Nusinow, David; Zhai, Bo; Rad, Ramin; Huttlin, Edward; Gygi, Steven
    Fewer than half of all tandem mass spectrometry (MS/MS) spectra acquired in shotgun proteomics experiments are typically matched to a peptide with high confidence. Here we determine the identity of unassigned peptides using an ultra-tolerant Sequest database search that allows peptide matching even with modifications of unknown masses up to ±500 Da. In a proteome-wide dataset on HEK293 cells (9,513 proteins and 396,736 peptides), this approach matched an additional 184,000 modified peptides, which were linked to biological and chemical modifications representing 523 distinct mass bins, including phosphorylation, glycosylation, and methylation. We localized all unknown modification masses to specific regions within a peptide. Known modifications were assigned to the correct amino acids with frequencies often >90%. We conclude that at least one third of unassigned spectra arise from peptides with substoichiometric modifications.
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    Induction of virulence factors in Giardia duodenalis independent of host attachment
    (Nature Publishing Group, 2016) Emery, Samantha J.; Mirzaei, Mehdi; Vuong, Daniel; Pascovici, Dana; Chick, Joel M.; Lacey, Ernest; Haynes, Paul A.
    Giardia duodenalis is responsible for the majority of parasitic gastroenteritis in humans worldwide. Host-parasite interaction models in vitro provide insights into disease and virulence and help us to understand pathogenesis. Using HT-29 intestinal epithelial cells (IEC) as a model we have demonstrated that initial sensitisation by host secretions reduces proclivity for trophozoite attachment, while inducing virulence factors. Host soluble factors triggered up-regulation of membrane and secreted proteins, including Tenascins, Cathepsin-B precursor, cystatin, and numerous Variant-specific Surface Proteins (VSPs). By comparison, host-cell attached trophozoites up-regulated intracellular pathways for ubiquitination, reactive oxygen species (ROS) detoxification and production of pyridoxal phosphate (PLP). We reason that these results demonstrate early pathogenesis in Giardia involves two independent host-parasite interactions. Motile trophozoites respond to soluble secreted signals, which deter attachment and induce expression of virulence factors. Trophozoites attached to host cells, in contrast, respond by up-regulating intracellular pathways involved in clearance of ROS, thus anticipating the host defence response.