Get hands-on experience starting DDA mass spectrometer files, running a peptide search with MS Amanda, building a spectral library from the search results and finally extracting chromatograms for quantitative analysis from the MS1 spectra in the DDA files. In this tutorial, you will use the Skyline Peptide Search wizard to search 3 DDA data files acquired from a human whole cell lysate with the Sigma Alrich UPS1 standard mix of stable isotope-labeled proteins spiked in. You will set up Skyline to extract the precursor isotope chromatograms for all detected peptides from the MS1 spectra in the data files, and you will begin to inspect the results in Skyline. (19 pages)
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* - written on v20.2, updated for v21.1, v22.2, and v24.1
