Skip to Main Content

Mass Spectrometry




The ESI source is the standard atmospheric pressure ion source for the measurements of singly charged samples such as benzodiazepines, and multiple charged samples such as proteins, peptides, and nucleic acids. The sample solution is introduced through the nebulizer assembly into the spray chamber, where it is subjected to the ESI process by means of an electrical field between the inner chamber wall and the spray shield, and with the aid of a nebulizer gas (N2). Heated drying gas (N2), flowing in the opposite direction of the stream of droplets, entering the spray chamber, is used to aid volatilization, thus ionization, and to carry away any uncharged material (Apollo II ESI & Apollo II Dual ESI/MALDI FTMS Users Manual).





The APCI source is best used for the analysis of polar and non-polar analytes. APCI nebulization takes place in a heated vaporizer tube. The heat evaporates the spray droplets resulting in gas-phase solvent and sample molecules. On leaving the vaporizer tube, gas phase solvent molecules are ionized by a current regulated discharge from a corona needle. By transferring their charge, the solvent ions convert sample molecules to sample ions. This ionization process also requires a countercurrent flowing drying gas (Apollo II ESI & Apollo II Dual ESI/MALDI FTMS Users Manual).





DSAThe Direct Sample Analysis (DSA) is a type of ambient ionization source. Ambient mass spectrometry is classified by the ability to sample and ionize analytes directly from surfaces with little to no sample preparation. The DSA operates on principles of atmospheric pressure chemical ionization (APCI) and therefore is ideal for the analysis of moderately polar to non-polar small molecules. The DSA is fitted to the PerkinElmer AxION Time of Flight mass spectrometer. The DSA offers high throughput screening of a variety of compounds including explosives, pesticides, drugs of abuse, arson samples and more.



Matrix Assisted Laser Desorption Ionization is an ionization method that utilizes a chemical compound or mixture, the matrix, and a high energy laser to ionize an analyte of interest. Sample preparation for MALDI uses a metal plate with multiple porous areas where the sample and matrix are spotted. Matrices for MALDI absorb the UV light spectra, allowing them to become charged when exposed to the UV laser of the MALDI source. The charges placed on the matrix are passed to the analyte, ionizing it, and are dislodged from the MALDI plate allowing for mass analysis.



Bruker 12T Apex IV FT-ICR-MS


The Bruker 12T Apex IV Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) allows for unmatched capabilities including the most extensive fragmentation pathways comprised of IRMPD, ECD, SORI-CID, and QCID. Its ability to achieve ultra-high resolution (ca. 2 million) combined with the ability to have multiple ionization sources makes it very well suited for characterizations of small molecules. The 12T FT-ICR is based on the tendency of charged particles in a magnetic field to gyrate with a frequency that is proportional to their mass and charge. Computer software, apexControl, controls the instrument and its parameters, and is used to analyze the results. Both ESI and APCI sources are used on this instrument. In order to be run on the 12T FT-ICR, samples must be dissolved in a solvent that is at least mass spectrometry grade or better. Solvents preferred for analysis are water, methanol, and acetonitrile. Other solvents may be used, but please discuss them with Josh Wilhide. If neat samples are being submitted, please provide at least 0.1 mg for low res, and at least 1 mg for high res. If already prepared samples are being dropped off, please provide them in appropriate containers (glass for small molecule and plastic for larger biomolecules). The facility does not allow this instrument to be run without assistance, but MCAC employees will run any submitted samples and create reports relaying the results of each sample.


Bruker Autoflex TOF with MALDI

bruker autoflex tof

The Bruker Autoflex Time of Flight (TOF) mass spectrometer coupled with Matrix Assisted Laser Desorption Ionization (MALDI) is used for analyzing biomolecules and large organic molecules. Although other instruments have difficulty in analyzing species of high molecular mass, the MALDI is designed to ionize such species that would normally be difficult to ionize. As a result, any intact biopolymer may be identified in a short amount of time. Combining the sample with a matrix on a MALDI plate, it is ionized by a laser to generate ions which are then separated by a mass to charge ratio. The matrix dilutes and isolates the analyte molecules from each other, and the laser irradiation functions as a mediator for energy absorption, causing ionization of the sample. Generally, crystalline solids of low vapor pressure are used as a matrix. In the TOF, ions of different m/z are dispersed in time during their flight along a field free path of known length, providing a complete mass spectrum. The TOF offers an unlimited m/z range, but may only be equipped with a MALDI source.



Bruker amaZon Speed Ion Trap (ASIP)

trapThe Bruker amaZon Speed Ion Trap (ASIP) performs several important functions, including mass accumulation, selective mass isolation, and excitation for collision induced dissociation and sequential mass ejection to produce a mass spectrum. In ion trap instruments, ions are generated outside the trap by ESI or APCI, which produces a continuous source of ions. The principles on which mass analysis is accomplished are based on the mass to charge ratio of the ions and not simply the mass alone. Because ions generated from an ESI interface often have multiple charges, any reference to mass measurement generally refers to m/z values (amaZon Series User Manual). The instrument is controlled by trapControl software. As an ion trap with UHPLC scan rates, the amaZon produces shorter run times and improved resolution of chromatographically separated peaks. This allows for greater peptide and protein identifications, thus maximizing the turnaround time for proteomic experiments. This instrument may be equipped with ESI and APCI. In order to be run on the Amazon Speed Ion Trap, samples must be dissolved in a solvent that is at least mass spectrometry grade or better. Samples can be diluted in the MCAC where mass spec grade solvents are readily available. Solvents preferred for analysis are water, methanol, and acetonitrile. Other solvents may be used, but please discuss them with Josh Wilhide. The concentration of samples must be 0.1 mg/mL or less. Otherwise, the sample could cause costly damage to the instrument.


PerkinElmer AxION TOF with DSA
DSA MCACThe PerkinElmer Axion Time of Flight (TOF) coupled with a Direct Source Analysis (DSA) source offers increased resolution over other instruments, increasing confidence with mass measurements. The TOF was designed with a unique detector that allows it to quantitate samples from the UHPLC. This instrument may be equipped with ESI, APCI, and DSA. The DSA requires little to no sample preparation, and provides fast and accurate results. It is perfect for the analysis of solid or liquid samples that may be difficult to prepare for other instruments. It is also equipped with ESI and APCI sources, which require sample preparation.






PerkinElmer SQ 300

single quad

The PerkinElmer SQ 300 is a single quad that is designed for around-the-clock quantitation. It has UHPLC scan rates that increase the turnaround time by upwards of 10-fold, thus maximizing productivity. The SQ 300 may be equipped with ESI and APCI.










PerkinElmer Clarus 600 – Gas Chromatography Mass Spectrometer (GC-MS)

The PerkinElmer Clarus 600 GC-MS is the perfect instrument for all of your GC-MS needs. Gas chromatography (GC) is a widely used quantitative technique responsible for separation, identification, and quantitation of pure and/or complex samples.  The principle of GC involves the volatilization of compatible analytes by heating the sample, and transporting components via a gaseous mobile phase and through an appropriate column containing stationary phase. Here, the mass spectrometer (MS) is a versatile, high-throughput detector alongside the GC which ionizes the sample, resulting in a mass spectrum.  The GC-MS is divided into several major components including: sample inlet, GC column oven, ion source, mass analyzer, and detector.  This particular instrument has an option for two ionization sources, electron impact (EI) and chemical ionization (CI).  The mass analyzer used here is a quadrupole, which serves to filter and/or accelerate the ions from the ionization source directly into the MS.  Both instruments above are connected to a compatible computer with Clarus 600 software for data processing and analysis. The software for the instrumentation is TurboMass, and additional touch screens are located on the instruments.

Samples most compatible for GC/MS use are volatile to semi-volatile samples.  Samples must be liquid samples dissolved in a solvent that is at least mass spectrometry grade or better.  Typical solvents for analysis are water, methanol, and acetonitrile.  Alternative sample introduction techniques for the instrument can be used with Headspace Trap and Thermal Desorption accessories capable for solid and/or gaseous samples.


PerkinElmer NexION 300D with ICP


The PerkinElmer NexION 300D is a single quad mass spectrometer coupled with Inductively Couple Plasma (ICP) ionization. This makes it a unique piece of equipment as it is able to perform trace analysis on salt and metal ions, which play an important role in environmental analysis, as well as nano scale preparations. This instrument is only equipped with ICP ionization.





Thermo Scientific LTQ XL ETD

The Thermo Scientific Liner Trap Quadropole (LTQ) XL an ion trap, which unlike the Bruker amaZon, offers multiple tandem pathways including ETD (non-ergotic) and CID (ergotic). These pathways facilitate the identification of post-translational modification in proteins. This instrument also features a nano flow HPLC setup for ultra low flow rates, allowing for less sample consumption. This instrument may be equipped with ESI, nano ESI, and APCI. Although it is used mainly for characterizing and quantifying proteins and peptides, the LTQ provides both sensitivity and flexibility.




PerkinElmer QSight Triple Quad

The PerkinElmer QSight is a triple quad, which by design makes it our most sensitive instrument. Sensitivity levels allow for limits of detection as low as 50 femto-moles injected onto the column. This low sensitivity becomes useful when studying metabolomics or other difficult samples. This instrument is equipped with ESI.