Equipment and rates

LTQ Orbitrap Velos ETD with Dionex Ultimate 3000 nano-LC

LTQ Orbitrap is a hybrid mass spectrometer which incorporates a linear ion trap and a high-resolution Orbitrap mass analyzers.  LTQ Orbitrap usually operates in data-dependent mode, i.e. a specified number of peptide precursor ions are selected for MS/MS based on their defined properties which are determined on the fly. These properties include precursor ion charge, mass, m/z, or a known modification. In a routine proteomics experiment, ten most abundant ions are selected for MS/MS every second and then excluded from selection for a specified time: 15-60 s depending on a chromatographic peak width. The instrument is equipped with HCD cell for performing iTRAQ-based or TMT-based relative quantification and ETD ion activation for analysis of labile modifications.

Dionex Ultimate 3000 nano-LC system separates peptides prior to the MS analysis using two reverse-phase columns: a shorter desalting (or trapping) column and a longer analytical column. The system is capable of 2D LC in which peptides could be separated based on their charge (or some other property) in first dimension and based on hydropathicity in second dimension.

Internal use rate is $65/hr; typical analysis times vary from 1 hr (gel band, simple mixture) to 4+ hr (complex mixture). Direct infusion (no LC) use rate is $114/hr; typical analysis time is 5-10 min per infusion.

Ultraflextreme MALDI-TOF-TOF

Ultraflextreme is a matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometer equipped with a 1 kHz smartbeam-II laser (solid state, frequency-quadrupled Nd:YAG) which can be focused down to 10 micron for high spatial resolution. The Facility provides software support for the MALDI-TOF (or TOF-TOF) analysis of polymers (PolyTools), protein top-down sequencing and peptide de-novo sequencing (BioTools), glycan analysis (part of ProteinScape), and microorganism identification (Biotyper, by agreement with Animal Diagnostics Laboratory). 

Internal use rates are $97.50/hr (staff) and $43/hr (approved user); typical analysis time is 5 minutes/sample and depends on the type of analysis, number of samples, and sample quality. TOF-TOF analyses require more time than TOF analyses.

QTof Premier

QTof Premier is a quadrupole time-of-flight (TOF) mass spectrometer equipped with an electrospray ionization (ESI) ion source. QTof Premier is used most often for nominal and accurate mass analyses of intermediates and products of chemical synthesis.

Internal use rates are $23/hr (LC-MS) and $76.50/hr (direct infusion).

SpectraMax M5

The SpectraMax M5 Microplate Reader is a dual-monochromator, multi-detection, multi-mode instrument with a triple-mode cuvette port and 6-well to 384-well microplate reading
capability. Detection modalities are absorbance, fluorescence intensity, fluorescence polarization, time-resolved fluorescence, and luminescence.

MALDI Biotyper

The MALDI Biotyper identifies microorganisms by analyzing their intrinsic proteins using mass spectrometry. An individual colony from an overnight culture grown on an agar plate is picked using a wooden toothpick and transferred to a MALDI target. This sample is allowed to dry, and a microliter of a matrix solution is added to the sample. The organic solvent in the matrix solution extracts proteins from the microorganisms. The extracted proteins are mainly ribosomal proteins, present in high concentrations. Once the matrix has crystallized (10-15 min), sample preparation is complete and the samples are ready for analysis. For some microorganisms, it is necessary to perform a more extensive extraction, which adds another 10-15 minutes to the sample preparation procedure.

For more information and for sample submission guidelines, follow this link.

Laboratory for Isotopes and Metals in the Environment (LIME)

The Proteomics and Mass Spectrometry Core Facility does not perform elemental analysis or stable isotope analysis. For these analyses, please contact LIME.

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