Located within the Avera Health and Science Center’s laboratory and research wing, our facility is part of the Department of Chemistry, Biochemistry and Physics. The equipment is available to university faculty, staff, students and members of the public for a fee.
For availability and questions, please contact M. Nurul Islam.
Rates
| Instrument/Category | SDSU | Academic non-SDSU | Industry |
|---|---|---|---|
| LC-MS/MS: SCIEX 5500+ TQ | $35/hour | $70/hour | $140/hour |
| GC-MS/MS: Agilent 8890 GC, 7000E TQ/MS | $30/hour | $60/hour | $120/hour |
| Mass Spectrometry Facility Personnel Time* | $175/hour | $262.50/hour | $525/hour |
*Mass spectrometry facility personnel time encompasses requested activities specific to individual users, including face-to-face training, mobile phase preparation, column preparation, sequence setup, sample preparation, method development consultation and other user-requested services that require mass spectrometry facility personnel time. This does not include troubleshooting, preventive maintenance, etc.
Equipment
LC-MS/MS
Shimadzu UHPLC-AB SCIEX QTRAP 5500 Mass Spectrometer System
Specifications
- Mass range: m/z 5-1,250
- Resolution (m/Δm): 2,000
- Accuracy: 1 ppm
- Scan speed: 20,000 Da/s
- Polarity switching in 50 ms
- Ionization source: Electrospray ionization
- Mass analyzer: Triple quadrupole
Common Applications
- Fast LC/MS
- Metabolite identification
- Detection and confirmation of low level pesticides
- Protein/peptide quantitation for biomarker verification and validation
- Ultrafast and selective MRM scans mean you can target and quantify thousands of compounds in a single analysis
Q-TOF LC-MS/MS (Accurate Mass)
Specifications
- Mass range: m/z 50-40,000
- Resolution (m/Δm): 30,000-50,000 FWHM
- Accuracy: <1-2 ppm (sub-ppm with automated real-time lock mass reference calibration)
- Scan speed: 50-100 spectra/s
- Ionization source: Dual electrospray ionization (ESI)/jet stream source
- Mass analyzer: Quadrupole time-of-flight
GC-MS/MS
Agilent 8890 GC + 7000E Triple Quadrupole
Specifications
- Mass range: m/z 10-1050
- MRM speed: 800 MRM transitions/s
- Minimum MRM dwell time: 0.5 ms
- Ionization source: Electron impact ionization, hydroInert ion source
- Mass analyzer: Triple quadrupole
- Mode of operation: EI (standard), CI (optional)
- Inlet: Split and splitless mode
- Sample introduction: Liquid, headspace and solid-phase microextraction
- Software: MassHunter (data acquisition and analysis)
Common Applications
- Environmental contaminants such as PCBs, PAHs and pesticides
- Food safety, quality and authenticity
- Materials testing and consumer products, including structural and functional characterization of materials, and detection, identification and management of impurities
- Energy and chemical applications, including crude oil refining and cleanup
- Pharmaceuticals, including impurities and APIs
- Forensic toxicology, including chemical warfare agents, trace analysis in fire debris and drugs of abuse
For all untargeted workflows, detected features and compound assignments are generally reported as putative annotations unless confirmed using authentic reference standards, retention-time matching and/or additional orthogonal evidence. Method suitability, sample preparation, reporting level and quantitative capability should be discussed with CMSF using the primary contact information below before sample submission.
Targeted Environmental Contaminants Analysis
EPA Method 1633: PFAS Analysis in Water by LC–MS/MS
Quantitative analysis of per- and polyfluoroalkyl substances (PFAS) in water samples using EPA Method 1633 applying liquid chromatography-tandem mass spectrometry (LC-MS/MS). The method supports measurement of a broad panel of targeted PFAS compounds (PFASs) in aqueous matrices, with appropriate quality-control procedures for trace-level analysis.
Targeted Chemical Profiling
Fatty Acid Ester Profiling by GC–MS
Identification and relative or quantitative profiling of fatty acid following methylationin biological samples using gas chromatography-mass spectrometry (GC-MS). This method chromatographically resolves fatty acid ester species based on their physicochemical properties and provides characteristic mass-spectral information to support compound identification and comparative profiling across samples.
Monosaccharide Analysis by GC-MS
Compositional analysis of monosaccharides in carbohydrate-containing samples or biological matrices by GC-MS after alditol acetate derivatization. Polysaccharides or glycoconjugates are first subjected to acid hydrolysis to release constituent monosaccharide, which are converted to volatile alditol acetate derivatives for chromatographic separation and mass-spectral detection. This approach allows to characterize the relative abundance of common neutral and amino monosaccharides.
Carbohydrate → Hydrolysis → Reduction → Alditol → Acetylation → GC-MS
Untargeted Omics Profiling
Untargeted Metabolomics by High-Resolution LC/Qtof-MS
High-resolution liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (LC/Qtof-MS) enables broad, discovery-oriented profiling of small molecules in complex biological samples. The workflow detects a wide range of metabolite features and provides accurate-mass and fragmentation data to support putative metabolite annotation, comparison among sample groups, biomarker discovery and pathogenesis profiling for a wide range of diseases.
Untargeted Lipidomics by High-Resolution LC/Qtof-MS
Comprehensive, discovery-oriented profiling of lipid molecular species using high-resolution LC/Qtof-MS. This method detects diverse lipid classes — including glycerolipids, phospholipids, sphingolipids, fatty acids and conjugates, and sterol and its esters, depending on extraction and acquisition conditions and supports relative comparison of lipid features across samples. Accurate-mass and MS/MS data support putative lipid identification and supports relative comparisons of lipid features across samples. Accurate mass and MS/MS data are used for putative lipid identification.
Accurate-Mass Compound Characterization
High-Resolution Accurate-Mass Measurement of Synthetic Compounds by LC/Qtof-MS-QTOF-MS
High-resolution LC/Qtof-MS provides accurate-mass analysis and molecular-formula confirmation of synthetic compounds. Samples are chromatographically separated before high-resolution mass analysis, allowing determination of precursor ion masses, isotope patterns and, when applicable, tandem MS information. Applications include identity confirmation, purity assessment, reaction monitoring, and characterization of synthetic products and related impurities.
Please direct all inquiries to our Mass Spectrometry Facility coordinator. If M. Nurul Islam is not reachable, contact the Department of Chemistry, Biochemistry and Physics.
