Proteomics sample taking

Both the capillary LC and NMR are controlled by the interface software, which enables the operator to use the UV-detector output for peak selection. Only peaks of interest can be subjected to NMR analysis, while minor or unimportant compounds can be directed to waste. NMR acquisition can take place in either on-flow or stop-flow mode. The combination of capillary LC and NMR is suitable for sample-limited applications (e.g., proteomics) and allows for low nanograms detection. 

The main challenge in the area is to visualize as many proteins as possible while maintaining the density of polypeptidic spots in two-dimensional gels at a manageable level. We have to take into account that each gel maps the protein content of a single sample and that the goal of most experiment in proteomic analysis is to compare several samples, that is, several gels. 

Not all the changes observed in a proteomic experiment will be related to toxicity some will be adaptive. While more difficult to conduct, it is important to recognise that more useful information may be gained from clinical research and every effort should be made to facilitate this. Such studies may take the form of collecting samples (blood, urine) from all subjects in a clinical trial for retrospective analysis when the outcomes of exposure are known. Alternatively it would be possible to establish tissue banks (of blood, urine, skin or liver biopsies) from patients with clinically well characterised ADRs. 

Therefore, the most popular approach to interpret such MS/MS spectra in a high-throughput manner uses DB searches with software tools known as search engines to find the best PSMs. As input, a search engine takes MS/MS spectra and searches them against reference proteomes of strains that are expected to be related to the sample with a twofold purpose first, to find PSMs which confidently decode tandem mass spectra and second, to quantify the contribution of DB reference microbes to the decoded spectral data set... 

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