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ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration.
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http://dx.doi.org/10.1093/nar/gkm371 | DOI Listing |
J Proteome Res
July 2023
Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France.
Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits from improvements in fractionation, separation, fragmentation, and mass analysis. The algorithms to match MS/MS to sequences have undergone a parallel evolution, with both spectral alignment and match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification (ProSight PD, TopPIC, MSPathFinderT, and pTop) in their yield of PrSMs while controlling false discovery rate.
View Article and Find Full Text PDFProteomics
April 2015
Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern, University, Evanston, IL, USA.
Many top-down proteomics experiments focus on identifying and localizing PTMs and other potential sources of “mass shift” on a known protein sequence. A simple application to match ion masses and facilitate the iterative hypothesis testing of PTM presence and location would assist with the data analysis in these experiments. ProSight Lite is a free software tool for matching a single candidate sequence against a set of mass spectrometric observations.
View Article and Find Full Text PDFCurr Protoc Bioinformatics
September 2007
University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
ProSight PTM v2.0, neuroProSight, and the Sequence Gazer allow the identification and characterization of proteins from high mass accuracy tandem mass spectrometric data of intact proteins and large peptides. Input data consists of one or more neutral precursor ion masses and a set of neutral b/y or c/z(.
View Article and Find Full Text PDFNucleic Acids Res
July 2007
Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.
ProSight PTM 2.0 (http://prosightptm2.scs.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
December 2005
Thermo Electron Corporation, San Jose, California, USA.
An automated top-down approach including data-dependent MS(3) experiment for protein identification/characterization is described. A mixture of wild-type yeast proteins has been separated on-line using reverse-phase liquid chromatography and introduced into a hybrid linear ion trap (LTQ) Fourier transform ion cylclotron resonance (FTICR) mass spectrometer, where the most abundant molecular ions were automatically isolated and fragmented. The MS(2) spectra were interpreted by an automated algorithm and the resulting fragment mass values were uploaded to the ProSight PTM search engine to identify three yeast proteins, two of which were found to be modified.
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