PatternLab V Handles Multiplex Spectra in Shotgun Proteomic Searches and Increases Identification.
Milan Avila ClasenMarlon Dias Mariano SantosLouise Ulrich KurtJuliana de S da G FischerAmanda C Camillo-AndradeLucas Albuquerque SalesTatiana de Arruda Campos Brasil de SouzaDiogo Borges LimaFabio C GozzoRichard Hemmi ValenteRosario DuranValmir C BarbosaPaulo Costa CarvalhoPublished in: Journal of the American Society for Mass Spectrometry (2023)
Complex protein mixtures typically generate many tandem mass spectra produced by different peptides coisolated in the gas phase. Widely adopted proteomic data analysis environments usually fail to identify most of these spectra, succeeding at best in identifying only one of the multiple cofragmenting peptides. We present PatternLab V (PLV), an updated version of PatternLab that integrates the YADA 3 deconvolution algorithm to handle such cases efficiently. In general, we expect an increase of 10% in spectral identifications when dealing with complex proteomic samples. PLV is freely available at http://patternlabforproteomics.org.