Mass Spectrometry

Overview of Services

This Core is housed within the MUSC Mass Spectrometry Facility which provides expertise, services, education, and training to enhance biomedical research endeavors through mass spectrometry-based proteomics. Currently there are over 50 investigators which utilize the facility for protein identification and characterization. Protein analysis includes in-gel or in-solution protease digestion, chromatographic separation and tandem mass spectrometric analysis of the resulting peptides, and interpretation of MS/MS data using Sequest , Mascot,  Protein Pilot, MaxQuant, and other search algorithms. The facility also assists in the development of customized applications for the isolation, detection and characterization of posttranslationally modified peptides (e.g. phosphorylation, glycosylation, oxidation, glutathionylation, and O-GlcNAc modification). With the recent acquisition of the Orbitrap Elite Mass Spectrometer we are expanding our services to couple quantitative approaches (SILAC, iTRAQ®, ICAT®, TMT®) to modification-specific experiments (eg.,phosphoproteomics, redox proteomics). We are developing methodology to analyze alterations in posttranslational regulation that impact signal transduction, epigenetic modulation, and the response to therapeutics with the goal of enabling investigators to discover molecular mechanisms underlying disease progression and therapeutic responses that may not be revealed through genomic studies.


Services: MALDI-TOF MS, LC-MS, and LC-MS/MS tandem mass spectrometry analyses are offered for protein analysis.  Protein identification services include in-gel or in-solution protease digestion, chromatographic separation and tandem mass spectrometric analysis of the resulting peptides, and interpretation of MS/MS data using Sequest® or Mascot® software. The facility will also assist in the development of customized applications for the isolation, detection and characterization of posttranslationally modified peptides (e.g. phosphorylation, glycosylation, oxidation, glutathionylation, and O-GlcNAc modification).  Sites of modification are verified by manual inspection of the data.  Please consult facility staff for feasibility and pricing of quantitative proteomic experiments (iTRAQ, TMT, Iodo-TMT or SILAC), the implementation of specialized approaches with quantitative proteomics (e.g. phosphoproteomics, O-GlcNAc proteomics), and MALDI-imaging mass spectrometry for tissue imaging experiments.                                         

 

Database searching is accomplished with Mascot (v. 2.4 via an in-house 24 CPU 64 GB RAM cluster), MaxQuant (via a 24 core 48 GB RAM high performance server), Byonic, SEQUEST (via BioWorks and Proteome Discoverer), and X!Tandem (via an in-house 6 CPU cluster). Additional custom Perl, Python, R and Matlab conversion tools are available to allow for broad down-stream compatibility.  All workflows incorporate additional search algorithms and tools as needed (e.g.,x. phospho site motif analysis).  Results from multiple search algorithms can be combined and post-processed using ProteoIQ and Scaffold, or with built-in tools within Mascot (i.e., percolator) and extensive custom work-flow options within Proteome Discoverer.  Analysis of isotope labeling experiments (TMT, SILAC, iTRAQ) is possible with iQuantitator, ProteoIQ, Scaffold and Proteome Discoverer.  Spectra from MALDI experiments can be processed using Progenesis MALDI, R-packages from Bioconductor, and in-house R-packages. MALDI imaging data is analyzed using FlexAnalysis 3.1 and FlexImaging 4.0 software from Bruker Daltonics, Multiple high-performance workstations are available to utilize these tools for each type of analysis.  All processed data are available for user-side analysis using free viewers for most of these programs.


       


Leadership

Director:  Lauren E. Ball, Ph.D.; 843-792-4513, ballle@musc.edu

 

Lab Manager:  Jennifer Bethard, M.S.; 843-792-8637, bethard@musc.edu

 

Computational Proteomics:  Ben Neely, Ph.D; neely@musc.edu


Staff: Susana Comte-Walters and Kim Norris-Caneda


Location and hours of operation

Hours Location

Available for Consults         

Wednesday 1:00PM

CRI 314

305 Children’s Research Institute

Charleston, SC 29425

Links and Resources

  1. Mass Spectrometry Facility 

Contacts

Name Role Phone Email Location
Jennifer Bethard
Lab Manager
 
843-792-8637
 
bethard@musc.edu
 
CRI 309
 
Ben Neely
Computational Proteomics
 

 
neely@musc.edu
 

 
John Baatz
Gel Proteomics
 
843-792-1049
 
baatzje@musc.edu
 

 

Services

Name Description Price
Training Request 

Initiate a training request to recieve training on any of these three pieces of equipment.

  • Bruker Autoflex III Imaging MALDI-TOF-TOF
  • Bruker Autoflex III MALDI-TOF
  • Thermo LTQ  (ESI-linear IT)
 
*
LC-MS/MS medium gradient 

moderately complex mixture - medium gradient

Orbitrap Elite

Digestion Included

 
*
2D LC-MS/MS (10 fractions) 

(10 fractions) ($125/salt step/sample)

 
*
2D LC-MS/MS (5 fractions) 

(5 fractions) ($125/salt step/sample)

Digestion included

 
*
4-Plex iTraq 

Contact Lauren Ball for consulation and pricing

 
*
8-plex iTRQ    *
Computational Proteomics 

Consult with Ben Neely initially to discuss customized data analysis and interpretation. For iTRAQ or TMT experiments, results can be post processed using iQuantitator. Other post-processing includes ProteoIQ. For comparative proteomic experiments statistical analysis, ROC curve analysis, supervised machine learning approaches, and unsupervised clustering analysis can be performed. This analysis includes basic data visualization including volcano plots, PCA plots, hierarchical clustering, and heatmaps. For biomarker discovery, performance measures can be included as well as implementing user specific approaches. Downstream analytical workflows can also include GO term analysis, pathway enrichment (KEGG, Wikipathway, Pathway Commons), transcription factor target analysis (MSigDB), ChIP enrichment analysis, kinase enrichment analysis, and reactome analysis. This list is not exhaustive. High quality figures for publication may also be generated.

 
*
De Novo Sequencing analysis    *
Determination of occupancy 

To determine % occupancy of a modfication

 
*
Iodo TMT    *
LC-MS/MS fast gradient 

(gel spot/band) fast gradient

Digestion included

 
*
LC-MS/MS long gradient 

complex mixture or PTM analysis - long gradient

Digestion included

 
*
LTQ Identification 

gel band or spot protein identifications

low resolution data

 

 
*
MALDI Imaging 
Contact  Rick Drake or Ellen Jones  for a consulation and pricing
 
*
MW Determination ESI    *
MWD by MALDI-TOF MS 1-3 Samples 

1-3 Samples

 
*
MWD by MALDI-TOF MS 4-6 Samples 

4-6 Samples

 
*
Phospho SILAC 

Contact Lauren Ball for consultation and pricing

 
*
Phosphorylation enrichment and analysis    *
Phosphorylation or PTM analysis    *
SILAC 

Contact Lauren Ball for Consulation and Pricing

 
*
TMT 

Contact Lauren Ball for consultation and pricing

 
*

Services


Search available services: View: by category alphabetically
Computational Proteomics (1)
MALDI Imaging (1)
Molecular Weight Determination (3)
PTM Quantitaton (2)
Protein Characterization (3)
Protein Identification (6)
Protein Quantitation (5)