Fill out the appropriate form each time you submit samples for analysis. Forms for (small molecule link) and (proteins/peptides link) can be downloaded as a pdf or Excel file. Samples will not be returned unless specifically requested.

Sample preparation has a direct impact on the quality of mass spectra.  Non-volatile salts, buffers and detergents can interfere with analyses, especially if analyzed by direct infusion.  Co-elution of certain salts and buffers with the analyte can result in ion suppression or buildup contaminants in the instrument, leading to spurious results and extensive instrument down-time.

A list of commonly used compounds that can interfere with electrospray ionization-mass spectrometry (ESI-MS) can be found at: http://masspec.scripps.edu/Services/Proteomics/salttol.php.  Solvents which should never be used include dimethyl sulfoxide (DMSO) and dimethylformamide (DMF) due to their high viscosity and interaction with instrument tubing.  Always use spectroscopic grade solvents and HPLC-grade water.  Volatile solvents such as methanol and acetonitrile are the preferred.  Detergents, phosphate or sulfate buffers and polyethylene glycols should be avoided.  Less than 1 mM salt and buffer is recommended, although ammonium acetate can be tolerated up to 20 mM.  Even at 0.1% concentration, trifluoroacetate (TFA) begins to suppress ion formation, so use other acids (acetic acid, HCl) as necessary.

Protocols compatible with mass spectrometry of proteins and peptides can be found at  http://goodlett.proteomics.washington.edu/protocols/.   Gel staining methods compatible with tryptic digestion and subsequent mass spectrometric analysis are summarized at
Always wear gloves and, if possible, work in a laminar flow hood to minimize keratin contamination.  Keratin from hair, skin and dust can easily overwhelm signals from the protein(s) of interest.

One hundred femtomoles or less of peptide samples are usually sufficient for protein identification(s), but 1-2 picomoles is preferred if available (100 ng of a 100 KDa protein = one picomole).  For comparison, the detection limit of Coomassie blue is ca. 100 ng.  For proteins up to 30-50 KDa, the suggested sample size is 50-100 microliters of a 20-50 micromolar solution.

The 4000Q Trap System.

The HEI Mass Spectrometry Center currently has a 4000 Q Trap LC/MS/MS system from Applied Biosystems.  This is a high performance hybrid triple quadrupole/linear ion trap mass spectromete useful for small organic molecule, peptide and protein analysis.  It is interfaced with  a 2-dimensional nano-LC liquid chromatograph, allowing characterization of complex biological samples.

Small molecules should be shipped when possible either as solids or neat oils in inertly sealed screw-cap vials.  Gel slices proteins and peptides should be shipped in siliconized or other high quality polypropylene tubes.  Do not use glass tubes. <Protocol>

House Ear Institute
Mass Spectrometry
Atten: James Kerwin
2100 W. 3rd Street
Los Angles, CA 90057