Mass Spectrometry/Proteomics

James A.  Mobley, Ph.D. – Director

Contact: (205) 996-6363


Facility Description

The UAB Mass Spectrometry/Proteomics (MSP) Shared Facility offers access to capabilities which are not available in individual Cancer Center member laboratories. The goal of the MSP Shared Facility is to provide state-of-the-art capabilities and training in mass spectrometry, proteomics, and bioanalytic technologies to support the research needs of UAB Cancer Center members.  The MSP Shared Facility supports the research efforts of Cancer Center members in each of the seven scientific programs.

A major theme of this facility is informatics, and for this reason we have a rack of 8 high speed servers that are coupled to a multimode cluster for analysis of high density data sets. We also offer a long list of software packages for automated data processing. These include numerous statistical packages (MatLab, SPSS, Statistica), Peptidomics driven analysis software (Refiner/ Analyst, Genedata), MzXML converters (i.e., ReAdW, Mzwiff, CompassXport)  matching algorithms (SEQUEST, MASCOT, X!TANDEM), Filtering & Quantification Software (Protein Prophet, XPRESS), de-novo approaches (i.e., Rapid de novo, Bruker Daltronics), and 2D PAGE analysis (Samespots, Nonlinear Dynamics) that will be working under a LIMS system (CPAS, LabKey) that we have currently implemented.

We are able to offer many applications for protein identification, analysis of post-translational modifications, and targeted or global quantification (relative or absolute measurements). We carry out automated proteomics experiments on global and PTM enriched proteins using a combination of non-tagged approaches, such as a) 2D-PAGE (Samespots)/ HTP-MALDI-TOF/TOF, and b) LCMS(MS)n (MS Refiner, Gendata), in addition to heavy label approaches such as a) stable isotope standard peptides (AQUA) and b) metabolic heavy labels (i.e. SILAC).  The final analysis which generates a list of protein ID’s is analyzed using various statistical applications and then run through a systems biology analysis platform (GeneGo) to determine the biological significance and connection between each class of proteins.

Services and Rates

Per Sample Costs Per Hour Costs
Measuring Protein Concentration $3.50 Cryo-sectioning & Histology $100.00
Cell/Tissue Homogenization $15.50 Chemical Labeling/Derivatization $100.00
1D Gel Separation $3.50 HPLC Separations (Offline) $100.00
Enzymatic Digestion $7.00 Methods Development $100.00
Solid Phase Extraction $3.50 Phospho Enrichment $100.00
Centrifugal Filtration $7.50 General Sample Prep $100.00
2D PAGE (11 cm) $75.00
Quantification & Statistical Analysis $100.00
MALDI-MS $7.00 Systems Biology $100.00
MALDI-TOF/TOF MS $45.00 Programming Time (For special projects) $100.00
LC-QTRAP 4000 or Triple Quadrupole $65.00 Generating Reports & Data QC $100.00
LC-LTQ XL with CID/ETD $85.00

Mass Spectrometry Charge Back Covers:  disposables, QC stds and blanks, mass spectrometer, HPLC, and autosampler time, service contracts, computer software/ hardware, personnel time for running the MS and for IT.

Per sample costs are greatly reduced due to our strict weekly workflow shown on our web site, were we only accept samples on Monday-Tuesday, in which case all samples are worked up at the same time starting on Wednesday, with MS analysis initiated on Friday each week, and posting of data to our LIMS in most cases early the following week. However, for most data sets, we do allow 10-15 working days once samples are submitted to get final data posted.

For those that would like to have their sample analysis expedited we are happy to do that at the per hour charge back fee of $100/ hr. In addition, the per-hour fees include disposables and most kits used, additional MS based analysis, quality controls, standards, etc. Informatics-based fees are quoted on a quarter hour bases and usual require less than an hour for the full analysis.

Contact Information:

Director:  James Mobley, Ph.D.


Phone: (205) 996-6363


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