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The analysis is performed on reverse phase chromatography coupled directly to high resolution mass spectrometer. The MS-MS spectra are used for Mascot database searching. The data are searched against in-house protein databases downloaded from UniProt containing all known non-redundant protein sequences or custom designed databases.
The Mascot software finds matching peptides in the database by their peptide masses and peptide fragment masses. The peptide identification is based on a probability-scoring algorithm (www.matrixscience.com) and the significant best matching peptide is shown in the Results.
The identified database peptide sequences are shown in the Results together with the obtained mass spectrometric peptide maps. The peptides used for the identification are highlighted in the sequence and the matching peptides are listed for comparison of the determined and calculated values.
Lyophilize or speed vac the peptide to a solid sample to increase peptide stability during shipment.
Alternatively, freeze the sample or refrigerate to +4 oC for cold shipment of the liquid sample.
Avoid detergents, DMSO, glycerol and other non-volatile solvents. Keep buffer concentration at a minimum as high salt will interfere with the ionization in the MS. LC-ESI MS can be done on samples containing small amounts of salts or urea, but the best results are obtained with low buffer strength in volatile solvents without detergents.
Use Eppendorf Safe Lock tubes or similar high-quality tubes from your lab.
OBS. If your sample contains any type of detergent, send us a request through the contact form to hear about the analytical capabilities for your project.
