Current Instrumentation

• ThermoFinnigan LCQ Deca XP+ ion trap LC-MS
• ThermoFinnigan LCQ "Classic" ion trap LC-MS
• Micromass Q-Tof hybrid quadrupole-time of flight LC-MS
• Micromass Quattro Premier triple quadrupole LC-MS
• Micromass ZQ single quadrupole LC-MS
• Agilent (HP) 6890/5973 GC-MS
• Advion NanoMate nano-electrospray robot
• Eksigent NanoLC-2D capillary HPLC

Other Instrumentation & Pictures

• The MS and the spider

The LCQ Deca XP+ is used primarily for proteomic applications, including protein identification, detailed peptide mapping, and MudPIT; long column capillary chromatography is used for peptide mapping and MudPIT analysis. Identification of proteins is performed on proteolytic digests by means of nanoflow LC-MS/MS with subsequent database searches using software packages such as Mascot and Sequest.

The LCQ "Classic" mass spectrometer is used for molecular weight determination and MSn analysis by direct injection of analyte solutions. It is also operated in-line with a Surveyor analytical HPLC and photodiode array UV detector. A wide variety of materials, including small molecules, peptides, proteins, and oligonucleotides, are analyzed on the LCQ.

The Micromass Q-Tof is applied to the identification of proteins and post-translational modifications, MudPIT, de novo peptide sequencing, intact protein analysis, and static nanospray H/D exchange studies (HXMS), as well as to exact mass determination (HRMS) for small molecules.

The Micromass Quattro employs an Agilent 1100 as the HPLC front end. This instrument specializes in quantitative work and selective assays of compounds of interest from complex matrices such as serum, tissue, and cell cultures.

The Micromass ZQ LC-MS and Agilent GC-MS are open access instruments. Please see our open access page for information on training and use of these instruments.

The Advion NanoMate is an automated chip-based nano-electrospray device. The NanoMate TriVersa is featured in automated hydrogen/deuterium exchange mass spec (HXMS) studies of protein folding landscapes (poster .pdf); the infusion capabilities are also used in antibody and other intact protein characterization and HRMS. The LC coupling enables the use of the NanoMate for LC-MS with optional fraction collection. See SUMS' NanoMate pictures.

The Eksigent NanoLC-2D is a splitless HPLC system with two sets of binary gradient pumps optimized for flow rates of 1-20 uL/min from the high flow pumps, and 50-1000 nL/min from the low flow pumps. The NanoLC-2D is used for reverse phase separations with a trap and column setup, as well as for MudPIT with a triphasic trap and long capillary column; the flexibility of the Eksigent system also enables other unique configurations (details in Posters & Presentations section). See SUMS' Eksigent pictures.

See below for instrument specifications and further description regarding ionization methods, mass range, resolution, and tandem and higher order MS.

IONIZATION. The mass spectrometers are equipped with electrospray (ESI) and atmospheric pressure chemical ionization (APCI) sources. ESI and APCI are both "soft" ionization methods, in which the molecular ion generally remains intact. (Electron impact ionization, such as that found in the GC-MS, is an example of a "hard" ionization method, in which compounds typically fragment upon ionization, and the molecular ion is weak or nonexistent.) Polar compounds such as amines, peptides, and proteins are best ionized by ESI. Non-polar compounds such as hydrocarbons and steroids usually give better results with APCI. Nanospray (NSI) is a low-flow version of electrospray, and does not require the use of heat or desolvation gas. Typical nanospray flow rates range from 1 uL/min down to 50 nL/min.

Commonly observed ions are (M+H)+, (M+Na)+, (2M+H)+ and (2M+Na)+ in positive ionization mode, and (M-H)- and (2M-H)- in negative ionization mode. Many compounds, particularly peptides and proteins, pick up multiple charges, and a distribution of charge states can be observed.

MASS RANGE. The quadrupole based mass spectrometers operate at an optimal m/z (mass to charge ratio) range of 50-2000. The Q-Tof MS has a significantly higher m/z range. Because electrospray ionization typically produces multiply charged ions, it is possible to analyze compounds of up to MW 150,000 Daltons.

RESOLUTION. At full scan, the quadrupole-based mass spectrometers give slightly better than unit resolution. Reducing the scan range and/or scan speed improves resolution to near 0.3 m/z, which allows the identification of singly, doubly, or triply charged ions. The higher resolution of the Q-Tof enables +5 and higher charge states to be distinguished.

Protein molecular masses, which are obtained by deconvoluting a series of multiply charged ion peaks, are accurate to within 0.02% and have been measured up to 150 kDa.

TANDEM & HIGHER ORDER MS. The ion traps, Q-Tof, and triple quad mass spectrometers all have MS/MS capabilities. The ion trap instruments can additionally perform MSn experiments, which are useful in obtaining structural information. In a typical MS/MS experiment, a selected ion is isolated and fragmented. The daughter ions which are generated depend on the structure of the parent ion. This process can be repeated by isolating and fragmenting a daughter ion in an MS3 experiment, and so on. The instruments are theoretically capable of MS10, but the value of n is typically limited to 3 or 4, because of the diminishing ion abundance as n increases.

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Last Modified 4.6.07

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