Chemical and Proteomic Mass Spectrometry Core Facility

Staged Reopening: Return to Research Update for Users

The purpose of the CPMSC facility is to provide state-of-the-art services and expertise for faculty and student researchers at Virginia Commonwealth University, as well as investigators at other institutes and private companies, for sample analysis with mass spectrometry. The facility has a growing number of mass spectrometers and ancillary equipment which allows us to design projects to meet the evolving needs of the investigator. We encourage investigators to contact the Mass Spec Core regarding their experimental needs so that we can discuss how to get the best results for you.

Basic mass measurement

Service is typically provided by the LTQ-Orbitrap for the confirmation of a known analyte or investigation of the elemental composition of an unknown. The sample is introduced by direct infusion to the ion source to obtain a high resolution/ low resolution mass spectrum of the analyte. Samples will need to be a minimum of 100 µL by volume with a concentration of 25-50 µM. The preferred solvent is pure water, but investigators may also choose to send samples dissolved in acetonitrile or methanol. It is important that the samples are salt free in order to get clear peaks of the analyte and avoid a clustered spectrum. Investigators who want to determine the molecular weight of an intact protein can also avail themselves of this service.

When an additional dimension is required to study a molecule, the ion mobility afforded by the Synapt G2-Si can be used. This separates molecules having the same m/z ratio based on their drift time, which is influenced by factors like molecular size and shape. The collisional cross section (CCS) of the ion can be determined using the IM-MS to study the chemical structure and three-dimensional conformation of the ions in gas phase. This is beneficial to study conformational changes of synthesized compounds, polymers, and heterogenous samples.


Fragmentation of the precursor ion, can be done to obtain additional and orthogonal information which may aid an investigator’s study of an unknown sample. A high collision energy produced by varying the Radio Frequency voltage, is applied to achieve the molecular dissociation of the precursor ion to product ions. The precursor ion can be pre-selected or may be the most abundant ion from the MS spectrum. The collision energy will be optimized by the facility staff to achieve the highest level of useful fragment ions.


Service can be utilized when the sample is a mixture requiring a separation or contains a high concentration of salts. The samples are analyzed by coupling a UPLC to the mass spectrometer, enhancing the concentration of each analyte as it enters the mass spectrometer and reducing the complexity of the sample. This allows the CPMSCF to accept sample concentrations as low as 10 fmol/µL and volumes of less than 10 µL. The elution flow from the UPLC is ionized and analyzed by the mass spectrometer.

The resulting spectra will be given as a series of printouts or emailed to the investigator.

Exact mass measurement

Service is provided with the LTQ-Orbitrap Velos.   The Orbitrap mass spectrometer detects the m/z of ions based on their frequency of oscillation in the orbitrap cell.  This frequency is converted to m/z using Fourier transform.  As frequency is the most accurately measureable property, mass measurements based on frequency have the highest mass accuracy. When exact mass measurement is requested, the sample measurement is carefully optimized by facility staff, including tuning the ion optics to reduce space-charge effect, which results in higher mass accuracy and lower mass error.

Protein identification

Mass spectrometry supports analysis of proteins or peptides as analytes. At the CPMSC facility, protein-containing samples are accepted in gel or solution. 

The analysis is typically done by peptide-centric bottom up method; digestion with enzyme (usually trypsin), peptide separation by chromatography, MS of the peptide, fragmentation for acquisition of MS/MS spectra, and database search. The gel bands can range from a light silver stain to dark Coomassie bands. It is strongly advised to avoid keratin contamination during gel band cut. The investigator can also bring in the gel to cut the gel band of interest at the core facility. 

For complex protein mixtures, to achieve better peptide separation and a greater dynamic range, we can provide additional techniques like offline ion exchange chromatography, customization of the UPLC to longer gradients, and addition of ion mobility as an on-line orthogonal separation. The protein ID is generally performed with the Synapt G2-Si and the data search is done using the PLGS (ProteinLynx Global Server). The databases will be customized based on the research project requirement. 

The investigators will receive the list of proteins and the peptides detected as a SCAFFOLD file. Scaffold (ProteomeSoftware) is a free viewer that allows detailed evaluation and comparison of qualitative results from a sample across experiments. Charges for protein identification will be based on the complexity of the sample. Please review the sample preparation method that is suitable for a mass spectrometry analysis in the protocols, as some silver stain kits have poor protein recovery.

Protein Quantitation

At the CPMSC core facility, Progenesis QI software by Waters is available to rapidly and reliably perform relative quantification of proteins by label-free methods. Progenesis QI uses multi-group experimental designs with a menu-guided data processing workflow. A standard set of known peptides is added to the sample in known concentration and used to align the samples, taking advantage of software capability to identify unique peptides across the sample set. The experimental data can be grouped in-silico and the alignment parameters are assigned based on the sample ion intensity map with retention time and mass to charge ratio. This aggregate map is used to consistently detect and quantify features across all samples and create a data matrix with no missing values, irrespective of the number of samples or replicates. The investigator is provided with a list of proteins and peptides which have been identified across all sample sets, as well as the fold change of each protein based on the relative quantification of the peptides in that protein.  Quantification samples are typically run in triplicate, to provide statistics on technical replicates.

Post Translational Modification Identification

Protein post-translational modifications (PTMs), such as phosphorylation, ubiquitination, acetylation and methylation, play critical roles in diverse biological processes such as signaling and regulatory processes, protein activity and degradation, regulation of gene expression, etc. Post translational modification identification and localization are essential to study cellular biology, cell signaling pathways of human diseases and various other applications. Rapid protein phosphorylation is one dynamic PTM, playing a key role in many cellular processes. Ion suppression and low abundance can make it difficult to identify the phosphopeptides. Hence we can provide the enrichment of the phosphorylated isoforms prior to analysis either as phosphoproteins or phosphopeptides. Please discuss with the CPMSC facility staff about the project to develop a method that is suitable for your experiments.

Other services

We encourage investigators to arrange a meeting with the  to discuss their projects. Experiments not listed here, such as the elucidation of post-translational modifications or relative quantitation are viable projects for the Mass Spec Core but may require a longer turnaround time or a higher quantity of sample.

Facility director: 

Kristina T. Nelson