Mass Spectrometry Facility

The OKED Mass Spectrometry Facility located in the Biodesign Institute provides MS analysis to ASU research groups requiring analysis of protein, peptides and small molecules.  Researchers are encouraged to discuss their projects and sample preparation protocols with the facility manager for optimum results.

Mass Spectrometry Core Services:

Protein Identification (including modification)
• From solution/gel band /
• In-gel/In solution digestion

Molecular Weight Determination
• Intact proteins/peptides/small compounds

Sample Purification
• Ziptip or Similiar

Target Molecules Quantification
• Selected or Multiple reaction monitoring (SRM or MRM) analysis
• Method Development

Mass Spectrometry Core Equipment List

The Agilent 7000D GC-Triple Quadrupole

This mass spectrometer will come equipped with a CTC PAL3 autosampler,  EI and CI ion sources and MassHunter software. It can scan at up to 20,000 m/z units/s and can cover a m/z range of 10 to 1,050 with tunable quadrupole resolution as low as 0.4 Da. In MRM mode it handles 800 transitions/s with a minimum MRM dwell time of 0.5 msec; limits of detection in EI-MRM mode are as low as 4 fg octafluoronaphthalene on column.

Thermo TSQ Altis™ Triple Quadrupole MS with Vanquish UPLC

  • With its improved Active Ion Management(AIM™)technology, segmented quadrupoles, novel electron multipliers, and enhanced ion transmission tubes
  • Ultimate sensitivity for all molecular types in matrices ranging from simple to complex.
  • Ultrafast selected reaction monitoring (SRM) increases the amount of molecular quantifications in less time.

Thermo Orbitrap Fusion Lumos Tribrid MS with ETD coupled with Ultimate 3000 UPLC

  • The most advanced mass spectrometer for proteomics work flows
  • Latest innovation include the Advanced Peak Determination (APD) algorithm for improved data-dependent experiments 
  • 1,000,000 FWHM ultra-high resolution for improves structural elucidation and quantitation of isobaric compounds.


This tandem (TOF/TOF) mass spectrometry instrument is designed specifically for sensitive, high throughput protein and peptide identification and quantification, and molecular weight determination. Mass resolutions greater than 20,000, mass accuracies less than 20 ppm.


Agilent 1290 HPLC coupled to Agilent 6530 quadrupole/time-of-flight mass spectrometer provides high accuracy and sensitivity for MS and MS2 studies. It is used for all protein, and many small-molecule studies in the unit. Mass accuracy is less than 2 ppm. Wide dynamic range facilitates measurement of low-abundance components with background interference. 

LECO GCxGC Time of Flight (TOF)

The GCxGC offers you the resolving power of a GCxGC system combined with advanced software for an increase in efficiency and productivity for samples that are too complex for a single-channel detector system. Ideal for everyday quality control and production needs, these GCxGC systems provide you with all the tools necessary to achieve exceptional results.

OKED Mass Spectrometry Core Support

Service Support

  • Data analysis (including MassHunter software, Data Explorer, MarkerView, Proteome Discoverer)
  • Consultation on experimental design, sample preparation, and results interpretation.

Joint-Grants Collaboration

  • Support letter/Research project collaboration.
  • Scope of research areas: medical science, biological science and chemical science
  • Figures and written materials (proposal and manuscripts) support.


  1. Identification of purified peptides and proteins using peptide fingerprinting and sequencing
  2. Identification of protein bands from Coomassie or silver stained gels:  This includes reduction/alklylation of cysteines, in-gel digestion with trypsin, followed by MALDI-TOF/TOF analysis
  3. Identification of environmental contamination with GC-MS
  4. Multiple Reaction monitoring (MRM) for quantification of differentially expressed proteins and metabolic: MRM approach is employed for validating an analyte (e.g., a potential biomarker identified during discovery phase, or some small molecular such as pharmaceutical drug, pesticide) in a large cohort of samples.  It is performed using a triple-quadrapole instrument (ABI4000 Triple quadrupole mass spectrometry or LTQ ).  The targeted ions are selected and fragmented. The fragment ion is quantified with high specificity and sensitivity. The isotope labeled standard is spiked into sample for the quantification.