The MUSC Mass Spectrometry Facility provides expertise, services, education, and state-of-the-art instrumentation to enhance biomedical research endeavors through LC-MS/MS-based proteomics. Services are offered for protein identification; characterization of post-translational modifications; and quantitative proteomics to identify differentially expressed/degraded proteins, regulated sites of post-translational modification, protein-protein interactions, and protein targets of drugs identified in phenotypic screens. Analyses include sample preparation, LC-MS/MS, database searching, generation of reports, and assistance with data interpretation. Faculty and staff assist with experimental design and the development/optimization of customized methodology for analysis of post-translationally modified peptides (e.g. phosphorylation and O-GlcNAc modification, N- and O-linked glycosylation, Cys modifications including S-glutathionylation, and glycation of Lys and Arg). Quantitative approaches including metabolic labeling (SILAC), isobaric tagging (iTRAQ/TMT), and label free proteomics (LFQ) are performed on the Orbitrap Elite or Orbitrap Fusion Lumos Mass Spectrometers. We are developing methodology to identify alterations in post-translational modifications that impact signal transduction, transcription, translation, and the response to therapeutics with the goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic response.

Contact Information

Lauren E. Ball, PhD, Director


Jennifer R. Bethard, MS, Facility Manager



Children’s Research Institute, Room 305

Medical University of South Carolina 

171 Ashley Ave., Charleston, SC 29425

Services & Pricing

Qualitative and quantitative discovery proteomic services are available for differential protein expression, protein interactions, biomarker discovery, and the identification of regulated sites of post-translational modification. Nano-scale, ultra high performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) is performed on high resolution and high mass accuracy, hybrid and tribrid orbitrap mass spectrometers. 

Quantitative targeted proteomics is available for verifying protein expression or measuring the extent of peptide/protein modification.  Isotopically labeled synthetic peptides serve as standards for quantification of the analyte of interest.  Multiple reaction monitoring (MRM) assays are performed by LC-MS/MS on a triple quadrupole mass spectrometer.

Please contact Jennifer Bethard ( regarding sample preparation, sample submission, and pricing. Please consult with Dr. Lauren Ball ( regarding feasibility, experimental design, expected results for quantitative proteomics experiments, and information for grant proposals.

Imaging mass spectrometry (IMS) is not currently offered as a core facility service. Please contact Dr. Richard Drake ( regarding MALDI-tissue imaging mass spectrometry and access to instrumentation dedicated to IMS.

Services Provided

Costs (MUSC Investigators)

Protein Identification

Simple or complex mixtures in solution or gel. Includes reduction, alkylation, digestion, C18 clean up.  *Number of proteins identified from 2ug Hela cell lysate on the Lumos MS.  Prices for Orbitrap Elite ETD MS or Orbitrap Fusion Lumos ETD/UVPD MS

· LC-MS/MS 60 min gradient. >2,000*

Elite: $130; Lumos: $230

· LC-MS/MS 120 min gradient. >3,000*

Elite: $190; Lumos: $290

· LC-MS/MS 180 min gradient. >3,500*

Elite: $250; Lumos: $350

MW Determination by Direct Infusion (Nanomate)


Single Protein Characterization

Includes reduction, alkylation, digestion, C18 clean up of protein in solution or gel.

· Identification of Post-Translational Modifications (180 min gradient)

Elite: $350; Lumos: $450/sample

· Relative Quantitation of Post-Translational Modifications (180 min gradient)

2 conditions x 3 replicates

Elite: $1,700; Lumos: $2,300

· Phosphopeptide enrichment and identification (180 min gradient)

Elite: $400; Lumos: $500/sample

· De Novo Sequencing/Extensive Inspection of Tandem Mass Spectra


Quantitative Proteomics (Unbiased, Discovery Proteomics)

Includes protein assay, reduction/alkylation, digestion, fractionation and or enrichment, quantitative LC-MS/MS, statistical analysis, and preliminary volcano plots and/or heat maps.  The number of replicates, fractions, and LC gradient length can be adjusted.

Differential Protein Expression or Abundance  Example pricing for projects:

· Label Free Proteomics. 60 min gradient:  $230 per sample + $250 for data processing ~500 proteins quantified

2 conditions x 3 biological replicates

Elite: $640; Lumos: $940. 

· Label Free Proteomics. 120 min gradient: $290 per sample + $250 for data processing (Recommended for protein interaction and affinity enrichment studies)

2 conditions x 3 biological replicates

Lumos: $1,990

· Label Free Proteomics. 180 min gradient: $350 per sample + $250 for data processing (Recommended for most studies including sorted cells) ~2000-4000 proteins quantified

2 conditions x 5 biological replicates

Lumos: $3,750

· TMT10 plex.  Includes reagents, labeling, bRP-LC separation into 12 fractions. 12 x 180 min gradient >6,000 proteins quantified

2 conditions x 5 biological replicates

Lumos: $6,600

Inquire for TMT11, TMT16 or iodoTMT

· SILAC.  bRP-LC fractionation into 12 fractions, 12 x 180 min gradient (Does not include media or labeled amino acids)

2 conditions x 1 biological replicate

Elite: $3,200/Biological replicate

Lumos: $4,400/ Biological replicate

Identification of Differentially Regulated Sites of Post-Translational Modification

· TMT10plex (e.g. phosphoproteomics) Includes reagents, labeling, bRP-LC separation into 12 fractions, TiO2 or affinity enrichment, 12 x 180 min gradient.

2 conditions x 5 biological replicates

Lumos: $9,069

(Does not include antibody)

· SILAC (e.g. phosphoproteomics) Includes SCX or bRP-LC separation into 12 fractions, TiO2 or affinity enrichment, and 12 x 180 min gradient

2 conditions x 1 biological replicate

Lumos: $4,950/Biological Replicate (Does not include media, amino acids, or antibody)

· Label free quantitation or analysis of other PTMs: O-GlcNAc, S-glutathionylation, ubiquitin, fucosylation, glycosylation, acetyl

Please inquire regarding feasibility and cost of enrichment reagents

Targeted Proteomics

2-3 heavy labeled synthetic peptides recommended per protein. Prices for Xevo TQ-S.  For projects necessitating higher sensitivity inquire for prices and availability on the Lumos.

· MRM method development

Please inquire

· MRM assay, 30 min gradient


· MRM assay, 60 min gradient


· MRM assay, 90 min gradient


· MRM data analysis (Skyline)


Other services

Manual inspection, de novo sequencing, and labeling of MS/MS spectra


Off-line preparative HPLC (strong cation exchange (SCX), high pH C18 reversed phase chromatography (bRP-LC))


New method development/optimization/extensive data processing


Additional information

For discovery proteomics, LC-MS/MS based services are currently provided using an Ultimate 3000 nano-LC in-line with an Orbitrap Elite ETD MS (ThermoScientific) or an Easy-nLC 1200 in-line with an Orbitrap Fusion Lumos MS.


Identification of peptides is based on a threshold of false discovery rate (FDR) < 0.01 when searching a forward and reversed, fully tryptic protein database. Generally peptides, modified peptides, and protein groups are identified with MaxQuant using FDR thresholds of < 0.01 at the PSM, peptide, and protein level. Sites of modification on target proteins of interest are manually verified.  For global studies, class I sites of modification with probability of site localization of >75% are reported. Label free quantitation and normalization, performed with the MaxQuant LFQ algorithm, is based on chromatographically resolved peak intensities rather than spectral counting.  Other search algorithms are used as needed (Protein Prospector, BioPharmaFinder, Byonic, Skyline, Proteome Discoverer with SEQUEST HT and Mascot). Normalized protein intensities are reported with fold changes and Student’s t test or ANOVA-derived p values adjusted for multiple hypothesis testing (q values). Statistical tests vary with the quantitative approach and experimental design. Reports include preliminary volcano plots and/or heatmaps.  Raw data are archived off site. For publication purposes and to comply with NIH data sharing policies, proteomics data are submitted to ProteomeXchange upon request.


Prices effective March 1, 2020