Facility Instrumentation
Each nESI instrument is coupled to two high performance nano-bore liquid chromatography systems (e.g. Dionex Ultimate 3000 RSLCnano UPLC, Proxeon EZ LC nano 1400, or Eksigent 425 nanoLC). Furthermore, the Thermo Q-Exactive is interfaced to state-of-the-art, automated lab-on-a-chip. Each chip may be designated to a single project to provide low femtomole sensitivities and eliminate cross contamination.
The Thermo Orbitrap LUMOS
The Thermo Orbitrap LUMOS was awarded via an HHMI technology grant (P.I.K. Campbell). It can achieve <1 ppm mass accuracy with four ion fragmentation methods at any step of MSn with sufficient sensitivity to make silver-stained gels analyses routine.
The Thermo Q-Exactive hf
The Thermo Q-Exactive hf quantifies proteomome response using Lable-free or SIL strategies and DDA or DIA while tracking nano-LC separations. It has the capacity to perform very sensitive quantitative studies using DDA, DIA or PRM which can be tuned to global discovery or exquisite specificity and resilience in high chemical backgrounds such CSF or vitreous humor, etc.
The Bruker Autoflex III MALDI TOF/TOF
The Bruker Autoflex III MALDI TOF/TOF provides sensitive characterization of modified peptides, saccharides and oligomers. Moreover, an offline Ultimate 3000 RSLCnano UPLC and a Proteineer fc II spotting robot are able to resolve complex samples and array the fractions on a MALDI target. Hence we can support differential proteome expression experiments with accurate mass and retention time tags (a MALDI-based, “label-free” approach).
We also provide accurate mass for intact biopolymers and rapid identification of bacterial cultures with the Autoflex III in the linear ion mode.
(Sub)milligram samples of complex proteomes may be prefractionated off-line using x100 ug loads and high pH reverse phase gradients which, even after concatenation, are physically complementary to the final on-line LC-MS/MS analysis.
Software
These multiple approaches are integrated with state-of-the-art software such as SEQUEST, MASCOT, MaxQuant, Scaffold and Perseus, that are orchestrated to yield high fidelity compound identifications, enhanced PTM coverage, precise expression analysis and may be further interrogated on Reactome.org, m/zCloud.org, and PDA to add a further dimension of annotation enrichment which can reveal biological network response.