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Series: Wiley-Interscience series on mass spectrometry. Show all links. Allow this favorite library to be seen by others Keep this favorite library private. Save Cancel. Find a copy in the library Finding libraries that hold this item Protein sequencing and identification using tandem mass spectrometry.
Reviews Editorial reviews. Publisher Synopsis "[the authors] present User-contributed reviews Add a review and share your thoughts with other readers. Analyses of this type are a fundamental part of most proteomics studies. The basic idea is to match tandem MS spectra obtained from a sample with equivalent theoretical spectra against a reference protein database.
The basic steps involved are:. The tutorial will finish with an exercise where you repeat the same protocol but with your own proteome as the reference database instead of using UniProt. Figure 9 - General flowchart of this training. The first part is to upload datasets to be investigated. Then the training will cover the key parts of the configuration of a X! Tandem search. Finally, we look at sorting and analysing the results.
The aim of the training will be to create a list of all proteins that can be confidently said to be present in the sample. This tutorial uses an E. The MGF data file is over MB, instead of downloading it to your computer, you can upload this file into Galaxy directly. To convert the file, follow the following steps: Download and Install ProteoWizard on your local computer. Note: version - Windows bit installer able to convert vendor files except T2D Start the ProteoWizard software on your local computer with windows operating system.
Warning : X! Other file formats have to be converted beforehand. A useful tool for that is msconvert 12 download : here. This tool only working on Windows. The output of X! Tandem is an XML format, which is not easy to decipher. In order to get a more readable file, we will convert the XML format to a table. This is a two step process:. Note: You can find all the details on the X! Tandem output file here: The file format for X!
The tandem XML file contains more information than the tabular format which can also be of further use e. Tandem website and X! Tandem documentation. Craig, R. Nesvizhskii, Alexey I. Mass Spectrometry Data Analysis in Proteomics Afgan, Enis et al. Nucleic Acids Res W1 : W3-W Apweiler, R. Nucleic Acids Research Mant, Colin T. Peptide Characterization and Application Protocols : Aebersold, Ruedi and Matthias Mann. Nature And, best of all, most of its cool features are free and easy to use.
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