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Department of Medicinal Chemistry


Recognizing the diversity of research interests on- and off-campus, the Center offers the following three “for fee” services to the scientific community: Submitted Sample Analysis; Investigator Instrument Use; and Protocol Development. A breakdown of charges for services under each category may be found under Rates.

Submitted Sample Analysis

Listed below are the types of analyses routinely performed by Center personnel on submitted samples. A rate schedule for these analyses may be found in Rates under Submitted Sample Analysis. Sample preparation and submission requirements are discussed in Sample Submission. Please contact the Center prior to submission of samples requiring “special” handling or analysis.

I LR (EI, CI, MALDI, ESI & APcI; ± eV)
Low Resolution (LR unit mass) analysis of gases, liquids and solids by an appropriate sample inlet system
II HR (ESI; ± eV)
High Resolution accurate mass measurement (AMM) coupled with empirical formula or amino acid determination; mass range < 2000 Dalton; Resolving Power (RP) 5000 – > 400,000.
III GC-MS, LR (EI, CI; ± eV)
Gas Chromatographic (capillary column GC) separation combined with LR mass spectral analysis; mass range < 1000 Dalton
IV LC-MS, LR (ESI & APcI; ± eV)
Liquid Chromatographic (LC) separation combined with LR mass spectral analysis; mass range < 3000 Dalton
V LR GC-MS, LC-MS and LC-MS/MS Quantification and/or Detection
GC or LC separation coupled with the selected ion monitoring (SIM), or selected and multiple reaction monitoring techniques, SRM and MRM, respectively, using tandem mass analyzers (MS/MS).
VI LC-MS/MS Structure Elucidation and/or Component Scouting
Use of collisionally induced dissociation (CID) in product (daughter) ion, precursor (parent) ion or neutral loss scanning analysis.
VII Intact Protein and Peptide Molecular Weight and Purity Determinations
Multiple charge state ESI spectra of a biopolymer(s) are deconvoluted to determine the zero charge mass of the component(s). (Depending on presence of salts, detergents or other ionic impurities in the sample, on-line LC-MS or other off-line cleanup procedures may be required.)
N.B. Ionization Modes (Instrument dependent)
EI electron ionization
CI chemical ionization
ESI electrospray ionization
APcI atmospheric pressure chemical ionization
MALDI matrix assisted laser desorption ionization

The last three methods are often useful when gas phase ionization techniques (EI & CI) are inappropriate due to the physical properties of a sample (non-volatile, thermally liable, etc.) or when the direct determination of molecular mass is not possible due to the absence of a molecular ion. See Ionization Methods and Operational Modes for more information relating Center instrumentation and capabilities.

Investigator Instrument Use

“Hands-on” instruction in the use of all Center instruments with the exceptions of the Micromass Q-Tof API-US and the Bruker Daltonics FTMS APEX III is available. The level of instruction is such that following the completion of training (usually 2 to 4 hrs) and several periods of supervised use, the researcher may exercise independent unattended use of an instrument with instructor approval. Instruction is instrument specific and is provided at the discretion of the management based on anticipated project or research group needs. Charges for instruction and investigator use may be found under Investigator Instrument Use.

Protocol Development

The Center offers both Sample Preparation and Mass Spectrometry Assay protocol development services. Dependent upon the need, assay protocol development may include: a methodology appropriate for sample preparation prior to MS analysis; a methodology for on-line LC- or GC-MS separations, if necessary; the running of preliminary Standard Curves, Reproducibility Studies; and the determination of Limits of Detection (LOD). The transfer of the final protocol to project personnel may also be included, however, complete validation of the method is not.

Protocol development services are provided at the discretion of the management and are based, in part, on the expectation that Center instrumentation will be used in carrying out subsequent studies. For information on the costs associated with this service, please check Rates under Protocol Development or contact Dale Whittington of our Staff.

The Center is not equipped or licensed to handle either biohazards or radioisotopes and, consequently, will NOT work with either pathogenic or radioactive materials. However, the Center will consult on sample preparations involving these media.

Quantitative Proteomics

We apply LC-MS/MS proteomics (MRM) for the quantification of proteins in complex biological systems, e.g., tissues, blood, urine and cerebrospinal fluid (CSF). The advantages of MRM proteomics are: i) selectivity, i.e., it can distinguish highly homologous proteins; ii) quantification of multiple proteins in a short time (approximately 10 proteins in 20 min) with almost similar or better sensitivity than western blotting; iii) antibodies are not required for quantification; iv) it offers absolute protein expression, and; v) data quality is better than western blotting as MRM relies on multiple signals, i.e., multiple peptides and multiple MRM transitions.

We offer research support to projects such as 1) targeted quantification of proteins (in tissues and biofluids) to investigate disease pathophysiology, and 2) discovery/validation of hypothesis driven biomarkers of diseases/drug efficacy and toxicity.

ADMET Quantitative Protein Assay Database, AQuPAD (coming soon)

Please contact Bhagwat Prasad or Dale Whittington.

Ionization Methods and Operational Modes

Positive and negative ions may be generated in all modes of ionization. The choice of an appropriate ionization mode and its polarity is dependent on the nature of the compound of interest (functional groups, volatility, stability, etc.) and on the method of sample introduction amenable to it.

In addition, the mass analyzer (time-of-flight, quadrupole, etc.) used in conjunction with a particular ionization and sample inlet technique will set limits on the resolution and mass range of the analysis. The following table attempts to give an overview of useful combinations based on the instrumentation available in the Center.

Ionization Mode EI CI ESI APcl MALDI
Mass Range Daltons (Da) 1 – 1,000 10 – 1,000 50 – > 60,000 50 – ~ 1,000 500 – 100,000
Analyte Polarity Low Low – Medium Medium – Very High Medium – High Low – Very High
Ion Charge electron Volts (eV) + ± ± ± ±
GC-MS Yes Yes No No No
LC-MS No No Yes Yes Yes
HR High Resolution No No Yes No No
CID Collision Induced Dissociation No No Yes Yes No