Chemistry Mass Spectrometry Facility

The Chemistry Mass Spectrometry facility serves researchers throughout the Texas A&M University system and the Department of Chemistry for chemical characterization. The services available include analyses of compounds ranging from small organic molecules to macromolecules including proteins, oligonucleotides, polymers and dendrimers. In addition, the research capabilities of the facility are accessible to non-Texas A&M users; academic, government and industry through a fee-for-service method.

All proteomics services are performed on the Thermo Scientific Orbitrap Fusion tribrid mass spectrometer equipped with a Dionex UltiMate 3000 reverse-phase nano-UHPLC system.

Protein Identification

We offer:

  • Identification of proteins from gel bands
  • Protein and peptide identification in solution, including identity confirmation of single, purified proteins, as well as large-scale protein identification in complex samples

Sample requirements

For gel samples, excise the band of interest and cut it into approximately 1-2 mm2 pieces. Place these in an Eppendorf tube and submit. Please provide an approximation of protein amount and information on the stain used in the submission form.

For in-solution samples, we require a minimum of 10 ug of protein for analysis. PEG, glycerol and detergents are not compatible with mass spectrometric analysis and must be removed prior to sample submission. Please provide details on the buffer composition in the submission form.

Quantitative Proteomics

As standard, we offer label-free quantitation (LFQ) as no specific sample pre-treatment is required. For LFQ, each sample is analyzed separately by LC-MS/MS and the results are subsequently compared across all samples to yield relative quantitation data.

Labeling of proteins for quantitation can be employed to enable multiplexed measurements (that is, samples are pooled together analyzed in a single LC-MS/MS experiment). There are several options for consideration:

  • SILAC (Stable isotope labeling by amino acids in cell culture) is suitable for comparing the abundance of proteins in cell culture under two different conditions. Labeling is performed at the cell culture stage during protein expression.
  • TMT (Tandem mass tags), iTRAQ and similar labeling systems can be used to label proteins and peptides following their extraction. A larger number of conditions (up to 11 for TMT) can be simultaneously compared.

Targeted quantitation of specific proteins for increased accuracy can be carried out by parallel reaction monitoring (PRM). PRM requires dedicated method development for each target and will thus be more time-consuming than other approaches.

Sample requirements

Requirements are similar to those for protein identification; we need a minimum of 10 ug of protein for analysis. We recommend submitting three biological replicates for quantitation.

Post-Translational Modification Analysis

We offer the identification and localization of acetylation, methylation, phosphorylation, glycosylation and other modifications by LC-MS/MS. Analysis of post-translational modifications can be performed as part of qualitative or quantitative experiments. In certain cases, enrichment of modified peptides may be necessary prior to sample submission.


Other, non-routine experiments may be developed and offered on an individual basis. If you wish to start a new project, please contact Klaudia Kocurek to schedule a consultation prior to submitting samples.

We provide mass spectrometry based analysis in fee-for-service format for the Texas A&M University Department of Chemistry, other departments throughout the university, and to researchers outside the university.
Our services include, but are not limited to mass analysis of small molecules including identification and structural elucidation, and mass analysis of macromolecules such polymers, dendrimers, and oligonucleotides. We have summarized our services as follows:


Analyses of small and macromolecules, which involve determination or confirmation of synthesized products, using low or high resolution mass spectrometry, are considered routine analysis. The following analyses methods are applicable for routine small molecule analysis:

Gas chromatography-mass spectrometry (GC-MS)

Thermo Scientific DSQ II

  • Low resolution mass measurements of volatile and thermally stable nonpolar compounds
  • Sources: electron ionization (EI), chemical ionization (CI)
  • Mass range: up to 1000 m/z
  • Sample introduction: standard GC sample injection, headspace, and direct probe
  • Service available daily

Liquid chromatography-mass spectrometry (LC-MS)

Thermo Scientific QE Focus

  • Separation of analyte mixtures coupled to high resolution mass measurements
  • Sources: electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI)
  • Mass range: up to 2000 m/z (3000 m/z in high mass mode)
  • Optional MS/MS fragmentation by HCD (higher-energy collisional dissociation)
    • Can confirm structural information
  • Service available daily

Direct infusion mass spectrometry

Thermo Scientific QE Focus

  • Fast, high resolution mass measurement for polar and relatively nonpolar compounds
  • Sources: electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI)
  • Mass range: up to 2000 m/z (3000 m/z in high mass mode)
  • Service available daily


Bruker microflex

  • Nominal mass measurements
  • High resolution mass measurements up to 5000 Da
  • Service available daily

Thermo Scientific Q Exactive Focus

High-resolution Orbitrap instrument configured for routine small molecule analysis.

  • LC system available
  • Architecture: hybrid quadrupole-orbitrap
  • Resolution: up to 70,000 at m/z 200
  • Mass range: up to 3000 m/z

Thermo Scientific Orbitrap Fusion

The primary proteomics instrument. Used for bottom-up proteomics analysis for simple and complex samples. Intact mass measurements possible for small proteins (up to approx. 50 kDa dependent on sample purity).

  • LC system available
  • Architecture: tribrid (quadrupole, ion trap, and orbitrap mass analysers)
  • Resolution: up to 500,000 at m/z 200
  • Mass range: up to 6000 m/z

Thermo Scientific Q Exactive

Secondary proteomics instrument.

  • LC system available
  • Architecture: hybrid quadrupole-orbitrap
  • Resolution: up to 140,000 at m/z 200
  • Mass range: up to 6000 m/z

Thermo Scientific DSQ II GC-MS

Gas chromatography platform.

Bruker microflex MALDI-TOF

Bruker amaZon SL

Dedicated training instrument. LC system available.