The Mass Spectrometry Core (MSC) facility maintained and operated by Office of Research and Innovation provides services and expertise for the analysis of small and large molecules to users across campus and to external users. Currently, the MSC facility consists of Waters Xevo-Qtof coupled with Acquity UPLC H-class or nanoAcquity UPLC M-class (NSF award number: 2018188), Agilent GCMS and SHIMADZU MALDI system.

Services and Rates

The core provides several levels of interaction with users such as: basic analytical services, experimental design, biostatistical analysis, guidance on mechanism-based analysis and ‘Omics Integration’ and custom services after consultation with users.

Under the Research Core Facility, Mass Spectrometry Core provides metabolites and protein characterization services for the UTD Research Community. Services include metabolite and protein identification and quantitation from a wide variety of sample types, from purified protein, simple mixtures to complex mixtures like cell lysates, tissue extract, and plasma. The facility is located on the first floor of the Bioengineering Sciences Building (BSB 11.533), 800 N Loop Rd, Richardson.

Effective on: 9/1/2023

Services Per sample (Internal User) Minimum sample size
Sample preparation Protein Extraction $25 3
Protein Quantification (DC method) $25 3
In-gel digestion $120 3
In-solution digestion $100 3
Existing LCMS Method (staff operated) 10 min gradient $15 2
30 min gradient $40 2
60 min gradient $80 2
90 min gradient $120 2
120 min gradient $160 2
200 min gradient $260 2
Data Analysis $30 2
New LCMS Method (staff operated) 30 min gradient $60 1
60 min gradient $90 1
Analysis $40 1
Bioinformatics Bioinformatics (Protein ID and Semi-quantification) $60 1
Bioinformatics (Up or down regulations) $60 6 (n=3|condition)
MS Technology Consultations $60/hour  
User Operated GCMS $41/hour  
MALDI $23/hour  

A 50% discount on GCMS or LCMS tools will be applied for bulk usage (> 25 monthly hours).

External academic prices are twice the listed price.

Industry prices are triple the listed price.

These are our official prices approved by the University. You can mix and match these, and it will give you some estimation of what your project will cost. You can download the table here. Contact our staff for an estimate of what each complete service costs.

To reserve an instrument, please visit the Lab Resources Scheduler. Name of the Faculty Supervisor/Sponsor and a valid Cost Center number is required to complete the reservation.

  • Users must make reservations before using the instruments.
  • Reservations must be cancelled at least 24 hours before the starting time of the reservation. Otherwise, the users will be charged for the reserved time slot.
  • Users are responsible for charges of unused reservation hours because of being late or for no-shows.
  • Users must not be more than 30 minutes late to prevent other users using your reserved time slot at your expense.
  • If a user cannot use the reserved slot for emergency reasons, please bring it to the staff’s attention.

Samples for QTof ESI MS

  • Mass Spec incompatible reagents: Reagents contain non-volatile electrolytes, which cause suppression of ESI signal and extensive adduct formation. Any incompatible reagents have to be removed prior to running the sample. NEVER wash MS bottles with DETERGENT. Never use dishwasher to wash MS bottles, rinse bottles with water and methanol, instead.
    • Detergents (e.g. SDS, Triton, Tween)
    • HEPES (or other non-volatile buffer) 
    • Non-volatile salts  
    • Non-volatile solvents (e.g. dimethylformamide (DMF), dimethyl sulfoxide (DMSO))
    • Tris-HCL
    • Phosphate buffers
    • Polyethylene glycol (PEG)  
    • Polymers
  • Important reminders to avoid keratin contamination for protein studies
  • Any sample preparation step prior to trypsin digestion should be done in a laminar flow hood. Wear nitrile (not latex) gloves and a lab coat.
  • ESI compatible solvents are water, methanol, acetonitrile, propanol, ethanol, toluene, dichloromethane, and nitromethane
  • Samples for ESI MS should be prepared using ultra-pure water (MilliQ 18MΩ cm, or LC-MS grade bottled water)
  • Protein solutions must be buffer exchanged to ESI-friendly solvent systems prior to mass analysis.

Sample Submission

New projects

Please arrange for a consultation with the core staff. The first step is to discuss the nature of the project by e-mail. The 2nd step is to have a meeting with the investigator and key associates. This meeting will define feasibility, period for the analyses, number of analyses expected, approach, sensitivity requirements, special issues, and labor for instrument setup, data acquisition and  data processing. Also, some discussions on sample treatment in a manner compatible with the mass spectrometry measurements (e.g. detection limit or removal of detergents) will be involved. This meeting will define any development work that needs to be performed. Effort in terms of time of personnel to develop methods will be estimated.

On-going projects

Contact the core staff to arrange for receiving additional samples. The core staff will be able to estimate the schedule for completing the analyses. The Facility person will also estimate the cost and ask details about sample preparations.

Costs for Sample Analyses

Fees for service depend on the amount of time per sample on the instrument, such as instrument set up time, method setup time, and time spend on database searching. Therefore, samples are typically group by assay type to limit instrument and UPLC change over between assays. Investigators that have repeating submissions of samples are encouraged to learn the data processing skills needed to analyze their data. The core staff is happy to train and assist in this process.

Data Analysis

Data processing is on a high-performance computer to evaluate the datasets generated from LCMS. We use PLGS, Progenesis QI (small molecule discovery analysis software) and Progenesis QI P (protein discovery analysis software) for our LCMS data analysis. We also use Skylines and MSstats with R for validations.

Seminars 2022 – 2023

  1. General LC Theory and Practice
  2. Method Development Basics
  3. Sample Preparation Protocols
  4. Single-Cell Proteomics (Part I)
  5. Single-Cell Proteomics (Part II)
  6. Metabolomics
  7. MALDI Imaging
  8. QTof technology

Need a Service?

Before sending your sample in, please email the core facility at to arrange a meeting. A sample submission form will be required so that we can better understand your needs.

Xevo G2-XS QTof Quadrupole Time-of-Flight Mass Spectrometry from Waters Corporation is designed for qualitative and quantitative UPLC-High Resolution Mass Spectrometry (HRMS) applications. Users can identify, quantify and confirm a range of compounds in the complex samples with the comprehensive qualitative information, in addition to the high quantitative sensitivity.

Meaningful information obtained from Data Independent Acquisition (DIA) and Data Dependent Acquisition (DDA) are used for hypothesis testing and hypothesis generation. Xevo G2-XS QTof feasures StepWaveTM ion optics with the XS Collision Cell provide a high sensitivity with no cost of selectivity. MSE delivers accurate mass precursor and fragment ion data for every detectable component.  This represents the ultimate in qualitative information, and because this DIA approach is un-targeted, the data can be interrogated again later as scientific questions evolve. In addition, Xevo G2-XS QTof features QuanTofTM technology to combine sensitivity and selectivity with the mass accuracy, dynamic range, and speed, and enhanced quantitative capability of Tof-MRM DDA data acquisition.


Our approach for protein analysis is “bottom-up” proteomics, where all proteins are proteolytically digested, producing peptide surrogates of the original proteins. Separations are performed on a nanoflow UPLC couple with nanaspray ESI source that have higher capacities for complex protein mixtures, e.g. cell lysates. This approach allows determination of femtomole amounts of proteins.

Protein quantitation can be accomplished using a ” label-free” technology that provides both relative quantitation (treatment vs. control) and absolute quantitation. Relative quantification of proteins is performed using addition of a protein standard, such as Alcohol dehydrogenase (ADH) from yeast. Alternatively, isotope-coded (labeled) peptides of interest can be added to the sample to provide relative quantitation information.

Peptide and protein identifications and quantification are performed using Protein Lynx Global Server (PLGS) and Nonlinear Progenesis QI for proteomics


Quantification of targeted small molecules, both metabolites and drugs. Assays are available for a range of metabolites for amino acids, sugars, nucleotides, intracellular metabolites, & fatty acids.

For most assays, stable isotopically labeled analogues are used as internal standards for precise quantification. The internal standards are added at the time of sample preparation to account for any sample extraction losses of analytes.

Detection limits range from high femtomoles to low picomoles. Detection limits in terms of concentration are defined by the amount of sample available, e.g. an assay with a quantification limit of 10 pmol would translate to a sensitivity of measurement of 10 pmol/µL for a 1 µL sample.

Untargeted metabolomics measurements. These measurements take advantage of the high mass accuracy of the QTOF and metabolite databases for identification of metabolites. Relative quantification is performed using Nonlinear Progenesis QI.

Vendors of Stable Isotopically Labeled Compounds


DDAData Dependent Acquisition
ESIElectrospray Ionization
LCMSLiquid Chromatography-Mass Spectrometry
MSMass Spectrometry
MRMMultiple Reaction Monitoring
UPLCUltra-High Performance Liquid Chromatography
QTOFQuadrupole-Time of Flight MS

Frequently Asked Questions

Below are FAQs regarding GCMS and MALDI services at the UTD. The list is not exhaustive. Please contact massspec@utdallas for further information should you need it.

Where are mass spec instruments located?

The instruments are located at BSB 11.541 (GCMS) and BSB 11.682 (MALDI)

What is a typical GCMS sample preparation procedure?

Usually, biological samples require isolation and modification steps before they are suitable for measurement by mass spectrometry. The modification step is performing the derivatization of a sample to change the analytes properties for better separation and enhance method sensitivity.

When is instrument training conducted, and how do I obtain training?

Instrument training is by appointment (

The length of time required for a training session depends on which instrument you are being trained on. A typical 3-4 hours are expected. During training, the operational principles and procedures for the instrument will be explained. A printed handout will be provided before the training.  A pre-recorded training video will be available if you can’t attend the training in person.

What is the procedure for instrument time booking?

To reserve an instrument, please visit the Lab Resources Scheduler. You need to provide the Faculty Supervisor/Sponsor name and a valid Cost Center number to complete the reservation.

First, you have to complete training on the device with the staff to book time on one of the self-service instruments (GC-MS/MaldiToF). Then, you will be entered into the on-line instrument scheduling system and will be allowed to log in with your NetID.

Instrument time is reserved using the lab resources scheduler.

If you cannot make your appointment, cancel your reservation time on the scheduler before it commences so that others may use the instrument.

Why did you charge me when I didn’t get a successful result?

We charge for every sample run, regardless of whether a result is expected. The only exception to this rule is where processing or instrument problems in the core have caused the lack of result.

Acknowledgement Guideline

Please use the phrase “We thank the Mass Spectrometry Core Facility at University of Texas at Dallas for the services to support this research” in the publication acknowledgement section.


Please contact Fang Bian by emailing with any questions or if you need further information.