Mass Spectrometry

The ARC MMA MS Lab houses instrumentation designed to generate mass spectra for a variety of different sample types and analytical needs. Sample introduction and separation methods are gas and liquid chromatography (GC and LC) as well as infusion, dried and thermal desorption modalities. Ionization sources onsite are effective for a wide range of molecular weights and functionality from small molecules to large bio and synthetic polymers (ESI, APCI, MMI, DART, MALDI, EI and CI). Mass analyzers in the MMA provide data for accurate mass (TOF) and fragmentation patterns (Q-TOF) for structure elucidation, and mass selective detection (single quads) and fragment filtering (triple quad) for targeted quantitative experiments. We also have stand-alone LC systems equipped with alternatives to MS detection (PDA, RI). MS Lab staff assist with consultation, user training, instrument maintenance, and instrument operation for full-service projects. 

  • Molecular Identification and Structure Determination: accurate mass analysis for the generation and confirmation of molecular formula and MS fragmentation patterns
  • Intact Protein Analysis: molecular weight confirmation and detection of protein modifications
  • Polymer Characterization: molecular weight characterization (from 0.5 kDa up to 500kDa) and end group analysis using MALDI-TOF for polymers that are generally difficult to ionize through other means
  • Biotyper Analysis: rapid and high throughput bacterial identification method using MALDI-TOF that compares the MS “fingerprint” of a bacterial colony to databases that contain the spectra of thousands of known bacterial species
  • Targeted Quantitative Analysis: relative or absolute quantitation of specific analytes
  • Untargeted Analysis: data-dependent, or data-independent acquisition of spectra processed with chemometric tools to understand changes in small molecule profiles in complex mixture under experimental or observational conditions
  • A full list of MS-based assays developed in the ARC can be found by clicking here

LC/MS Systems

  • Agilent 6230 UPLC TOF MS, the ‘B-TOF’: The B-TOF is primarily used for accurate mass analysis. Samples are introduced via an Agilent 1290 UPLC system with flow injection or column separation, or by infusion. Ionization can be performed with ESI, APCI or MMI (multimode ionization-combined ESI and APCI) sources. Samples may alternatively be introduced as a dried spot for DART ionization. The TOF mass analyzer provides accurate mass data with resolution 18,000 FWHM for m/z 1,522, and mass accuracy of +/-5 ppm. Software: Agilent Mass Hunter
  • Waters Xevo UPLC TQD MS, the ‘Xevo’: The Xevo is primarily used for targeted quantitative assays. Samples are introduced via a Waters Acquity H-class UPLC system with flow injection or column separation, or by infusion. Ionization may be done with ESI or APCI sources. Samples may also be introduced as a dried spot for ASAP ionization. The triple quadrupole mass analyzer performs mass selective fragmentation (MS/MS) for quantitative experiments with unit resolution and nominal mass accuracy. Software: Waters Mass Lynx, Target Lynx; training for open-source Skyline data processing is also available.
  • Bruker maXis UPLC Q-TOF MS, the‘maXis’: MaXis is primarily used for accurate mass analysis, intact protein analysis, structure determination and untargeted characterization. Samples are introduced via a Waters Acquity H-class UPLC system with flow injection or column separation, or by infusion, and ionized with ESI or APCI sources. The Q-TOF mass analyzer provides accurate mass and fragmentation (MS/MS) data with mass resolution up to72,000 and +/-2 ppm mass accuracy. Software: Bruker Compass. The maXis is a full-service instrument.

GC/MS Systems

  • Agilent 5973N GC/MS, the ‘GCMS’: The GCMSis primarily used for mass measurement and structure confirmation of volatile organic compounds. Samples are introduced via 7683 automatic liquid sampler and 6890 GC, ionized with EI followed by single quadrupole mass analysis with unit resolution and nominal mass accuracy. Low temperature option available using LN2 oven cooling. Software: Agilent Chemstation with Wiley MS spectral database.
  • Thermo ISQ TD CD/MS, the ‘ISQ’: The ISQ is primarily used for structure confirmation and quantitation of volatile samples requiring pre-concentration. Samples are introduced via a Markes Unity-xr thermal desorption unit designed for pre-concentrating volatile and semi-volatile organic compounds, or an autosampler 1310in line with a Trace 1310 GC followed by EI ionization and single quadrupole mass analysis with unit resolution and nominal mass accuracy. Software: Chromeleon with NIST MS spectral database.
  • Thermo TSQ GC/MS, the ‘TSQ’: The TSQ is primarily used for targeted quantitative assays for volatile compounds. Samples are introduced via a Triplus RSH autosampler, separated on a Trace 1310 GC, ionized by EI or CI followed by mass selection and filtering with a triple quadrupole mass analyzer with unit resolution and nominal mass accuracy. Software: Chromeleon with NIST MS spectral database; training for open-source Skyline data processing is also available

MALDI Systems

  • Bruker Micro FLEX LRF MALDI-TOF, the ‘MicroFLEX’: The MicroFLEX is primarily used for polymer and nanoparticle characterization, intact protein analysis and biotyper analysis. MALDI is also a useful ionization technique for small molecules (> 300 Da) that have limited/no solubility or are difficult to ionize through other means. For typical sample prep, dissolved samples are mixed with a matrix (typically UV absorbing organic acids to aid in ionization), spotted, and dried on a stainless-steel plate. A nitrogen laser focused on the sample spot prompts desorption and ionization; ions travel through a TOF mass analyzer. In reflector mode, which is suitable for samples that are generally less than10 kDa, the MicroFLEX offers resolution up to 15,000 with mass accuracy of +/-15 ppm. In linear mode, ionizable biological and polymer samples up to ~250 kDa can be observed (depending on the type of sample being analyzed, synthetic polymers are more challenging), however resolution and mass accuracy are lower in this mode. Software: Bruker FlexControl, FlexAnalysis, Compass MBT (for Biotyper) and PolyTools.
  • Bruker UltrafleXtreme MALDI-TOF, the ‘UltrafleX’: The “Ultraflex” is a state-of-the-art high resolution mass spectrometer well suited for the analysis of macromolecules like synthetic polymers, nanoparticles, proteins, peptides, and other biologically derived polymers, as well as small molecules. What makes this instrument unique from other MS techniques in the lab is the MALDI (matrix assisted laser desorption ionization) ionization technique that uses a 355 nm modified Nd:YAG laser paired with a small molecule UV absorber (the matrix) to volatilize and ionize large, insoluble, and/or labile molecules non-destructively. As a “soft” ionization mechanism, MALDI enables us to observe intact, singly charged molecules even at exceptionally high molecular weights (up to 500 kDa!). Our users enjoy the MALDI because it allows them to rapidly and accurately measure samples that are often difficult or impossible to analyze by more traditional mass spectrometry methods. The “Ultraflex” is capable of resolution exceeding 40,000, mass accuracy better than 5 ppm, and sensitivity in the femtomolar range. The MS/MS feature allows users to do advanced fragmentation for structure elucidation of samples up to 5 kDa. Our suite of synthetic polymer characterization software allows our polymer chemists to easily analyze their MALDI-TOF spectra to predict end groups and obtain information on average molecular weight, degree of polymerization, dispersity and more. Software: Bruker FlexControl, FlexAnalysis, PolyTools, Polymerix, BioTools and ClinProTools.

LC Systems

  • Waters Acquity UPLC-PDA the ‘UPLC’: The UPLC is primarily used for separations method development, when chromatography requires solutions or buffers that are not MS compatible, or when analytes are not ionizable or have light absorbing properties better suited for detection. Samples are introduced through an Acquity UPLC system with column separation followed by PDA (photodiode array) detection. Software: Waters MassLynx.
  • Waters 1525 HPLC, the ‘1525 LC’: The 1525 LC is a semi-preparative system for purification of target compounds in mixtures. Samples are introduced via Rheodyne injection followed by column separation, PDA and RI (refractive index) detection. Software: Waters Empower.

For Training on self-service instruments:

Training has a minimum charge of one hour of instrument and staff time.

Rates can be found here

Please use the iLab Portal to request a formal quote for equipment use or services.

Acknowledgment of facility contributions is expected in publications that include any data generated in the facility. Please cite us by our Research Resource ID (RRID:SCR_021758).

An example of an appropriate acknowledgment is:

“The authors wish to thank the Analytical Resources Core (RRID: SCR_021758) at Colorado State University for instrument access, training, and assistance with sample analysis”


MS Lab Data Management Plan

Scientific Staff:

Dr. Claudia Boot: MS Lab Manager; LC, GC and MS applications, training, and course support

Dr. Alyssa Winter May:  Soft Materials Postdoc; MALDI applications, and soft materials characterization support