Instrumentation
Resource instrumentation has been refined for leading-edge analyses of biological problems and is suitable for biochemical and chemical analysis, separations research, mass spectrometry, and molecular biology efforts. The Resource is equipped with an 11.4-tesla superconducting magnet high-performance Fourier transform ion cyclotron resonance (FTICR) instrument, with two complete mass spectrometer vacuum systems; as well as 3.5-, 7-, and two new 9.4-tesla FTICR instruments. Added features on each instrument include the (PNNL-developed) electrodynamic ion funnel, devices for external ion accumulation, and ultra-high-sensitivity electrospray ionization (ESI) sources. Instrumentation is described in detail below.
FTICR Instrumentation (interfaced with capillary Liquid Chromatography (LC) or electrophoresis for nano-scale separations)
11.4-tesla wide-bore high-performance FTICR mass spectrometer. This system provides ultra-high resolution, sensitivity, and dynamic range, and exploits a very low noise RF-shielded environment. Two independent vacuum systems allow all instrument modifications to be conducted without sacrificing experiment time. A completely separate work area is available for pump-down to high vacuum and system testing. The two vacuum systems can be switched in less than one day for use with the 11.4-tesla magnet.
Two 9.4-tesla high-performance, high-throughput FTICR mass spectrometers. A prototype high-throughput system is currently running with automated 24-hr/day operation with capillary LC-FTICR proteome analyses. Our added ion optics enable the dynamic selection of ions to be sent to the spectrometer using our Dynamic Range Enhancement Applied to Mass Spectrometry (DREAMS) technology to increase the dynamic range of the analysis. The LC system is a fully automated version of our ultra-high-pressure reversed-phase LC technology that incorporates a robot for automated sample selection and injection. A distributed communications package allows the data station to control the LC system for integrated operation of the LC-MS system. In addition, data sets from the instrument can be analyzed using our advanced software package, ICR-2LS. The second high-performance system has the addition of a larger cell and higher resolution external ion selection.
7-tesla ESI-FTICR mass spectrometer. This instrument, which employs RF-only quadrupoles to transmit ions from the external source to the trapped ion cell, has recently been upgraded by the addition of a new collisional-focusing ESI source and interface that provides improved sensitivity for both positive and negative ions. The instrument is currently used for LC-multiplexed tandem mass spectrometry (MS/MS) studies. Additional experiment flexibility is provided by the availability of an isolated dual FTICR cell assembly and a large format (12-cm diameter) cell. The vacuum chamber of this instrument employs a custom cryopanel-pump assembly, which provides extremely high pumping speeds enabling online applications.
3.5-tesla wide-bore FTICR mass spectrometer. Both of the vacuum chambers for the 11.4-tesla spectrometer have been designed to be directly compatible with the 3.5-tesla magnet. This interchangeable format allows prototyping of ion source, cell or detection schemes, and other instrument development activities at the lower magnetic field, allowing the most efficient usage of the 11.4-tesla magnet for demanding collaborative applications.
FTICR data stations. Each of the FTICR spectrometers has dedicated hybrid FTICR data stations. They consist of a commercially supported data station (Finnigan FT/MS ODYSSEY 4.0 or Bruker XMASS), which is utilized to control all aspects of pulse sequence generation and data acquisition, while a laboratory-built ancillary data station is used to generate additional waveforms for advanced ion manipulations.
Other Mass Spectrometers
Micromass Q-TOF Ultima. This state-of-the-art quadrupole time-of-flight (Q-TOF) spectrometer has an ESI source and combines the simplicity of a quadrupole [MS 1], the high-ion conductance of a hexapole collision cell, and the ultra-high efficiency of an orthogonal acceleration-TOF mass analyzer [MS 2] to achieve simultaneous detection of ions across the full mass range.
SCIEX QSTAR Pulsar. This system is a high-performance hybrid Q-TOF mass spectrometer. Specific scan modes such as precursor ion scanning, enabled by patented LINAC Pulsar collision cell technology, identify the type and location of post-translational modifications or drug metabolites with outstanding specificity and sensitivity. The NanoSpray ion source or capillary LC ion source provide progressively increased throughput for protein and peptide identification and characterization. The on-board analyst QS Software with Information-Dependent Acquisition enables unattended, automated MS to MS/MS acquisition for capillary LC-ESI applications. This instrument has been modified to incorporate our ESI interface and an electrodynamic ion funnel for improved sensitivity.
Six Finnigan LCQ ion trap mass spectrometers. These systems have capillary high-performance LC front ends for efforts requiring separations development prior to FTICR application. The mass spectrometers are equipped with ESI sources and controlled by Finnigan Xcalibur software, supporting MSn tandem experiments with Dynamic Exclusion. This facilitates the acquisition of MS/MS data from multiple components within a single chromatographic peak with up to 10 stages of dissociation.
Finnigan and SCIEX quadrupole mass spectrometers. Two research-grade triple quadrupole instruments are available, and are primarily used for technology and method development activities.
Additional Capabilities
All of the aforementioned spectrometers are on a common computer network with direct high-speed access to the EMSL data storage and archive facility, a multi-terabyte storage system that allows large numbers of data files to be archived indefinitely. Collaborators are able to access and download their data via the Internet and have access to other data at the discretion of the Resource staff and other collaborators.
The EMSL laboratories also include facilities for sample preparation and storage, chemical synthesis and derivatization, one-dimensional (1-D) and 2-D polyacrylamide gel electrophoresis, capillary electrophoresis (CE) and ESI-MS, and related instrumentation development and experimentation, purifications, synthesis, and biological research activities. Four CE systems are available, including three Crystal systems that are optimal for MS interfacing. The CE systems have electrical isolation and interlock and equipped with robotic injectors and a Pharmacia PhastSystem integrated planar electrophoresis system.
Other equipment includes an Applied Biosystems 270A integrated instrument and data system for CE with UV-Vis/absorbance detection and a Beckman P/ACE System 1000 CE instrument extensively modified for application with an ESI interface for mass spectrometry.
