Andrew Jarnucak’s PhD work now published in Molecular Omics. Joint study with Claire Eyers and Chris Grant, looking at the temporal effects on the quantitative proteome of heat shock and yes we see the usual suspects. My favourite feature of this nice dataset is the way it validates the protein interaction data generated by AP-MS methods – Fig6 in the paper shows this really well where the known chaperone targets track their parent chaperones really well. here
UK Chaperone club @ Leeds University just before Christmas 2017 was a nice meeting. My first time but I really liked the ethos of the meeting, which was to encourage junior staff and students to present and this made for an engaging day – despite the heavy colds in the room. My talk was rushed – apologies – but the paper is now out in Molecular Omics.
Enjoyable HUPO2017 in Dublin. We presented work on stop codon readthrough validation in Drosophila. Mike Nelson in the lab is writing it up now with over 150 protein extension events validated, at least via strong mass spec evidence. Lots of new datasets generated by Lilley lab too – hope to get these out to the community soon.
Dr Manuel Garcia Albornoz has joined the lab, looking at the bioinformatics and computational biology of yeast protein turnover in the context of succinate production, on a ERA-IB funded project called ECOYEAST. We are hoping to get stuck into quantitative proteomics data generated by colleagues in Liverpool at the CPR very soon.
After a colossal effort, our BBSRC-funded paper on absolute quantitation of the yeast proteome using QconCAT methodology is now in press at MCP. If you want to grab the main data in terms of copies per cell for ~1200 proteins (+ upper limits on a further ~600) then we’ve made the data available in excel format via MCP. Lots of interesting things came out of this study, including the estimates for total protein copies per cell, comparisons with other existing proteome quantitations, and the relationship between transcriptome and proteome (we also quantified the mRNA in the same cells via RNA-seq on the SOLiD system here at Manchester).
Proteomics data available from ProteomeXchange PXD002694
RNA-seq read data from GEO: accession GSE73898
(edited version of Fig5)
It’s all good
Congratulations to Dr Andrew Jarnuczak who recently graduated from the lab. He’s been working on quantitative proteomics of the chaperone system in yeast. We’ve one paper out and another submitted on heat shock response.
I attended a UKSG meeting last year and was persuaded to pontificate a bit about researcher perspectives on academic publishing and open access. It was an enjoyable meeting and good discussions were had. The upshot was that some brave soul typed up my talk and we edited it (a bit, but not too much) into shape for publicatin in Insight (their journal). It can be accessed here. The actual slide deck is UKSG-hubbard-nov-2014
As part of our CoPY project, the Liverpool team road-tested some kinase QconCATs on the TQS at Waters, and a nice report of their results is online. In short, the additional sensitivity allowed them to dig a bit deeper and obtain reliable quantitation information for a few more proteins. We worked hard to pick the right peptides here and this is a nice demo of how it can work well. Well done Philip et al.
After Christmas and exams, all systems are go for two new UG students in the lab who will be looking trying to improve methods for calibrating label-free proteomics data with absolute data from our CoPY project, and looking for patterns in our RIP-seq data for RNA-binding proteins, like Puf3. All in yeast of course.
Nothing to report, as yet. Just starting