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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Preprocessing MS data

Every time an ionized protein or peptide hits the detector, the instrument registers it. This ionized fragment has m/z, and the detectors measure the intensity of this fragment, which is called a mass spectrum. Mass spectra have several imperfections, which can complicate their interpretation. Detecting the peaks in these spectra is challenging because some peptides with low abundance may be buried by the noise, causing a high false positive rate of peak detection. The chemical, ionization, and electronic noise often results in a decreasing curve in the background of MS data, which is referred to as a baseline. The existence of a baseline produces a strong bias in peak detection. Therefore, it is desirable to normalize, smoothen, ...

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