Main category - Education
Sub category - Science
Developer - CompOmics
Filesize - 113459
Title - PeptideShaker
https://hideuri.com/qlDo6o
vers_1.16.40_PeptideShaker.dmg
PAPPSO FEATURE IMPROVEMENT: Updated Ensembl to version 86. BUG FIX: Added and to PeptideShaker command line option description. Make sure you backup your Mac to keep your important files, before taking next step, that erase your Mac’s Startup drive. PRIDE Converter 2 Tool still has problems converting my files - PeptideAtlas/PASSEL focusing on SRM/MRM datasets.
Official:
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PeptideProphet (TPP) Download Count: 50 Search engine result files: (called ‘SEARCH’): the original output files from your search engine or your analysis pipeline, Trans-Proteomic Pipeline (TPP) and/or files, or MaxQuant text output files, among many others. They should contain the peptide/protein identifications. In the submission tool they should be tagged as ‘SEARCH’. Alfred An algorithm for the assignment of phosphorylation sites in peptides is described. The program uses tandem mass spectrometry data in conjunction with the respective peptide sequences to calculate site probabilities for all potential phosphorylation sites. Tandem mass spectra from synthetic phosphopeptides were used for optimization of the scoring parameters employing all commonly used fragmentation techniques. Calculation of probabilities was adapted to the different fragmentation methods and to the maximum mass deviation of the analysis. The software includes a novel approach to peak extraction, required for matching experimental data to the theoretical values of all isoforms, by defining individual peak depths for the different regions of the tandem mass spectrum. Mixtures of synthetic phosphopeptides were used to validate the program by calculation of its false localization rate versus site probability cutoff characteristic. Notably, the empirical obtained precision was higher than indicated by the applied probability cutoff. In addition, the performance of the algorithm was compared to existing approaches to site localization such as Ascore. In order to assess the practical applicability of the algorithm to large data sets, phosphopeptides from a biological sample were analyzed, localizing more than 3000 nonredundant phosphorylation sites. Finally, the results obtained for the different fragmentation methods and localization tools were compared and discussed. General Error Diagnosis - If you go to Help and then Bug Report, you will find a log of the PeptideShaker activity. This includes transcripts of any errors that the application has encountered, and can be very useful in diagnosing issues. Proteios LIBRARY UPDATE: Updated mascotdatfile to version 3.4.2, such that the Mascot search results can be loaded again.
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