Its partner tool Peptide Shaker tool is then used to combine and evaluate the search engine results. In this tutorial we will use Search GUI tool, as it can automatically search the data using several search engines. Again, there are several software solutions for this, e.g. It is generally recommended to use more than one peptide search engine and use the combined results for the final peptide inference ( Shteynberg et al., 2013, Mol. Different peptide search engines have been developed to fulfill the matching procedure. There can be multiple PSMs per peptide, if the peptide was fragmented several times. Accordingly, a peptide that is successfully matched to a sequence is termed PSM (Peptide-Spectrum-Match). This step is called peptide-to-spectrum (also: spectrum-to-sequence) matching. To find out the peptide sequences, the MS2 spectrum is compared to a theoretical spectrum generated from a protein database. This method generates a spectrum of peptide fragment masses for each isolated peptide - an MS2 spectrum. Mass spectrometry experiments identify peptides by isolating them, ioinizing and subsequently colliding them with a gas for fragmentation. Afterwards, upload the resulting mzML file to your Galaxy history. You can find a detailed description of the necessary steps here (“Peak List Generation”). If msconvert tool is not available in your Galaxy instance, please install the software on a Windows computer and run the conversion locally. The vendor libraries used by msconvert are only licensed for Windows systems and are therefore rarely implemented in Galaxy instances. In the Advanced Options set the Output file type to MGF.
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