Mass spectrometry can be used for the structure elucidation and quantification of small molecules, like metabolites. Since the chemical nature of the compounds to be analyzed varies over a wide range, we help you with choosing a suitable method for each individual project. Since December 2013 we offer the possibility to directly analyze spots on TLC-plates. For more details compare the section "Devices/TLC-MS-Interface" of our homepage.
Protein identification is a standard service of the core facility. We make the tryptic digests of a gel-band or a sample in solution and analyze the resulting peptides with nanoHPLC-MS/MS. The customer gets a database search report for each sample. As search engines, we use MASCOT and SEQUEST.
For the analysis of post-translational modifications, we also digest the proteins of interest and analyze the peptide mixtures with nanoHPLC-MS/MS. Post-translational modifications are identified automatically by software packages if possible or by hand. For an enrichment of e.g. phosphopeptides, we use a special trap-column within the nanoHPLC. The analysis of the localization of the post-translational modification is sometimes difficult. Possibly, ECD-experiments help to assign the distinct amino acid.
Quantitative proteomics can be done with labels or label-free. In prinziple, we are able to analyze whole proteomes through 2D-nanoHPLC in one run. We have a software called SIEVE, which is used for label free quantification. For an absolute quantification, isotopicly-labeled standard peptides are required.
Mass determination of intact proteins can either be achieved by ESI-MS or by MALDI-TOF. ESI-MS usually results in a mass accuracy of +/- 2 Da, depending on the size of the proteins. With our mass spectrometers, we are able to analyze proteins up to ~ 100 kDa, depending on the ionization efficiency of the proteins. With MALDI, proteins > 100 kDa can be analyzed. Though, for ESI-MS we need high amounts. As a rule of thumb, 100-200 µg in not more than 100µL are required. MALDI is more sensitive, but not very accurate. Usually we desalt the proteins for mass determination with reversed phase chromatogtaphy. The proteins are denatured. If a native measurement is necessary, only low salt conditions will be accepted.