Mass Spectrometry Center
University of Washington * School of Pharmacy
Department of Medicinal Chemistry

SERVICES

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.

 

TYPE	DESCRIPTION
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.)
VIII	Peptide Analysis via LC-MS/MS (Gel Band Digest) The protolytic digest of a SDS-PAGE gel band is subjected to separation on a capillary LC coupled to the nano-spray (ESI) source of a tandem hybrid mass spectrometer (LTQ-FT, Q-TOF). The probable identity of the protein(s) is determined by the matching of sequence data obtained from the collisionally induced dissociation (CID) of selected peptide ions in the digest's chromatogram against those of candidate proteins found in a database, with a probability scoring given by the search engine.
IX	Peptide Analysis of Protein Complexes via LC-MS/MS (Shotgun Proteomic Profiling) A protolytic digest of a complex protein mixture is subjected to LC-MS/MS analysis as above (VIII). The probable identities of the proteins present are determined by the matching of sequence data obtained from the collisionally induced dissociation (CID) of selected peptide ions in the digest's chromatogram against those of candidate proteins found in a database, with a probability scoring given by the search engine.
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 Tom Kalhorn 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.

 

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	APcI	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
Further information concerning basic principles, instrumentation and literature of these and other ionization methods may be found at the University of Heidelberg Little Encyclopedia of Mass Spectrometry web site or by contacting the Center.

 

Instruments | Services | Contacts | Rates Sample Submission | Links | Home Department of Medicinal Chemistry School of Pharmacy | University of Washington   For more information about the Mass Spectrometry Center, contact Dale Whittington. For comments or suggestions on this web site, contact Caryl Lynch. Last updated: April 3, 2009