Facility Instrumentation

Each ESI instrument is coupled to a high performance nano-bore liquid chromatography system (e.g. two Agilent 1260s and an Dionex Ultimate 3000 RSLCnano UPLC). Furthermore, the Agilent instruments are interfaced to state-of-the-art, automated lab-on-a-chip platforms. Each chip may be designated to a single project to provide low femtomole sensitivities and eliminate cross contamination.

  • The Agilent 6530 quadrupole time-of flight (Q/TOF) can achieve <10 ppm mass accuracy and it has sufficient sensitivity to make analysis of silver-stained gels routine.
  • A Thermo LTQ-XL linear ion trap mass spectrometer with electron transfer dissociation (ETD) enables micro-sequencing for discovery and identification. We can also probe PTM in enriched targets using ETD, because the rapid kinetics of dissociation prevents subsequent scrambling in the gas phase fragments
  • Our Agilent 6410B triple quadrupole (3Q) has the capacity to perform very sensitive quantitative studies using multiple reaction monitoring (MRM) which is both specific and resilient in high chemical backgrounds such as sera and vitreous humor.
  • The Bruker Autoflex III MALDI TOF/TOF provides sensitive characterization of modified peptides, saccharides and oligomers. Using an offline Ultimate 3000 RSLCnano UPLC and a Proteineer fc II spotting robot, we 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  [Bruker UltraFleXtreme Thumb] “labelfree” approach). We have the same nanoLC system on our LTQ so that, after deconvolution, we can align both MALDI and ESI spectral information. The fractions arrayed on targets can be archived and re-studied over two weeks providing in depth “ion cartography” of tissue samples.
  • We also provide accurate mass for intact biopolymers and rapid identification of bacterial cultures with the Autoflex III in the linear ion mode.
  • We also have an atmospheric MALDI source for the LTQ XL with which we perform higher structural interrogation of lipid ions or glycopeptides.
  • Large gel sample sets are processed with a Genomic Solutions automated digester (the Progest).


These multiple approaches are integrated with state-of-the-art software (SEQUEST, MASCOT, Scaffold, Spectrum Mill and Mass Profiler Professional). Each adds a new dimension of specificity for positive compound identification, enhanced PTM coverage or more precise expression analysis.