Proteomics

Our earlier methods include gas-phase fractionation, the first practical data-independent acquisition method and large-scale label-free quantitation. At UVic the focus is single cells and very small numbers of cells: glycated hemoglobin in one red blood cell, immune and cancer cells from patients, and bacteria taken straight from urinary tract infections.

Four stacked panels: (a) a chromatogram with an arrow marking a small peak near 28 minutes; (b) and (c) mass spectra in which a few labelled ions stand among heavy noise; (d) a tandem mass spectrum labelled 649 (2+) — We developed several methods to extend detectable dynamic range, like the data-dependent acquisition method gas-phase fractionation (PMID: 12298092) that was inspired by the fact that even ions of low signal-to-noise can give high-quality tandem mass spectra (PMID: 12955739), while Brian Chait’s paper on “…hypothesis-driven multiple-stage mass spectrometry” (PMID: 15283590) on apparently empty regions of a mass spectrum led to the data-independent acquisition method PAcIFIC (PMID: 19572557).

Earlier methods

Integrating proteomic and genomic data in systems biology
11340206
Gas-phase fractionation, extending the detectable dynamic range
12298092
The first practical data-independent acquisition method, scanning every m/z channel
19572557
Large-scale label-free quantitation, without stable isotope labels
17952072 +1
Chemical crosslinking analysis without isotope labelling
18947195 +2

At UVic

Glycated hemoglobin quantified in a single red blood cell
Azad Eshghi
37093777
Profiling small numbers of immune and cancer cells from ovarian cancer ascites
Bo Ren, Kenneth Weke
42610661
How bacterial infection changes the host cell proteome
Bo Ren, Kenneth Weke
41116249
E. coli proteomes taken directly from patients with urinary tract infections
Linda Nartey, Kenneth Weke
41698857