Literature DB >> 29626295

UV-POSIT: Web-Based Tools for Rapid and Facile Structural Interpretation of Ultraviolet Photodissociation (UVPD) Mass Spectra.

Jake Rosenberg1, W Ryan Parker1, Michael B Cammarata1, Jennifer S Brodbelt2.   

Abstract

UV-POSIT (Ultraviolet Photodissociation Online Structure Interrogation Tools) is a suite of web-based tools designed to facilitate the rapid interpretation of data from native mass spectrometry experiments making use of 193 nm ultraviolet photodissociation (UVPD). The suite includes four separate utilities which assist in the calculation of fragment ion abundances as a function of backbone cleavage sites and sequence position; the localization of charge sites in intact proteins; the calculation of hydrogen elimination propensity for a-type fragment ions; and mass-offset searching of UVPD spectra to identify unknown modifications and assess false positive fragment identifications. UV-POSIT is implemented as a Python/Flask web application hosted at http://uv-posit.cm.utexas.edu . UV-POSIT is available under the MIT license, and the source code is available at https://github.com/jarosenb/UV_POSIT . Graphical Abstract.

Entities:  

Keywords:  Charge site; Native MS; Protein; Ultraviolet photodissociation

Year:  2018        PMID: 29626295      PMCID: PMC6004247          DOI: 10.1007/s13361-018-1918-x

Source DB:  PubMed          Journal:  J Am Soc Mass Spectrom        ISSN: 1044-0305            Impact factor:   3.109


  14 in total

Review 1.  Investigation of intact protein complexes by mass spectrometry.

Authors:  Albert J R Heck; Robert H H Van Den Heuvel
Journal:  Mass Spectrom Rev       Date:  2004 Sep-Oct       Impact factor: 10.946

Review 2.  The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes.

Authors:  Elisabetta Boeri Erba; Carlo Petosa
Journal:  Protein Sci       Date:  2015-03-31       Impact factor: 6.725

3.  Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

Authors:  Anton A Goloborodko; Lev I Levitsky; Mark V Ivanov; Mikhail V Gorshkov
Journal:  J Am Soc Mass Spectrom       Date:  2013-01-05       Impact factor: 3.109

4.  ProSight Lite: graphical software to analyze top-down mass spectrometry data.

Authors:  Ryan T Fellers; Joseph B Greer; Bryan P Early; Xiang Yu; Richard D LeDuc; Neil L Kelleher; Paul M Thomas
Journal:  Proteomics       Date:  2015-04       Impact factor: 3.984

5.  193 nm Ultraviolet Photodissociation Mass Spectrometry of Tetrameric Protein Complexes Provides Insight into Quaternary and Secondary Protein Topology.

Authors:  Lindsay J Morrison; Jennifer S Brodbelt
Journal:  J Am Chem Soc       Date:  2016-08-17       Impact factor: 15.419

6.  Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry.

Authors:  Michael B Cammarata; Ross Thyer; Jake Rosenberg; Andrew Ellington; Jennifer S Brodbelt
Journal:  J Am Chem Soc       Date:  2015-07-09       Impact factor: 15.419

7.  Characterization of hydrogen bonding motifs in proteins: hydrogen elimination monitoring by ultraviolet photodissociation mass spectrometry.

Authors:  Lindsay J Morrison; Wenrui Chai; Jake A Rosenberg; Graeme Henkelman; Jennifer S Brodbelt
Journal:  Phys Chem Chem Phys       Date:  2017-08-02       Impact factor: 3.676

8.  Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry.

Authors:  Lindsay J Morrison; Jennifer S Brodbelt
Journal:  Analyst       Date:  2015-11-24       Impact factor: 4.616

9.  Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies.

Authors:  Sem Tamara; Andrey Dyachenko; Kyle L Fort; Alexander A Makarov; Richard A Scheltema; Albert J R Heck
Journal:  J Am Chem Soc       Date:  2016-08-16       Impact factor: 15.419

10.  Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

Authors:  Navdeep Jaitly; Anoop Mayampurath; Kyle Littlefield; Joshua N Adkins; Gordon A Anderson; Richard D Smith
Journal:  BMC Bioinformatics       Date:  2009-03-17       Impact factor: 3.169

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  13 in total

1.  Enhanced Characterization of Membrane Protein Complexes by Ultraviolet Photodissociation Mass Spectrometry.

Authors:  Sarah N Sipe; John W Patrick; Arthur Laganowsky; Jennifer S Brodbelt
Journal:  Anal Chem       Date:  2019-12-10       Impact factor: 6.986

2.  Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry.

Authors:  Christopher M Crittenden; Elisa T Novelli; M Rachel Mehaffey; Gulan N Xu; David H Giles; Whitney A Fies; Kevin N Dalby; Lauren J Webb; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2020-04-21       Impact factor: 3.109

3.  Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules.

Authors:  Jennifer S Brodbelt; Lindsay J Morrison; Inês Santos
Journal:  Chem Rev       Date:  2019-12-18       Impact factor: 60.622

4.  Top-Down Analysis of Proteins in Low Charge States.

Authors:  Aarti Bashyal; James D Sanders; Dustin D Holden; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2019-02-22       Impact factor: 3.109

5.  Impact of charge state on 193 nm ultraviolet photodissociation of protein complexes.

Authors:  Sarah N Sipe; Jennifer S Brodbelt
Journal:  Phys Chem Chem Phys       Date:  2019-05-08       Impact factor: 3.676

6.  Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation.

Authors:  Luis A Macias; Sarah N Sipe; Inês C Santos; Aarti Bashyal; M Rachel Mehaffey; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2021-10-29       Impact factor: 3.109

7.  Symmetry of 4-Oxalocrotonate Tautomerase Trimers Influences Unfolding and Fragmentation in the Gas Phase.

Authors:  Sarah N Sipe; Emily B Lancaster; Jamie P Butalewicz; Christian P Whitman; Jennifer S Brodbelt
Journal:  J Am Chem Soc       Date:  2022-06-29       Impact factor: 16.383

8.  Exploring the Conformations and Binding Location of HMGA2·DNA Complexes Using Ion Mobility Spectrometry and 193 nm Ultraviolet Photodissociation Mass Spectrometry.

Authors:  Sarah N Sipe; Kevin Jeanne Dit Fouque; Alyssa Garabedian; Fenfei Leng; Francisco Fernandez-Lima; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2022-06-10       Impact factor: 3.262

9.  Structural Characterization of Carbonic Anhydrase-Arylsulfonamide Complexes Using Ultraviolet Photodissociation Mass Spectrometry.

Authors:  Inês C Santos; Jennifer S Brodbelt
Journal:  J Am Soc Mass Spectrom       Date:  2021-03-08       Impact factor: 3.262

10.  Investigation of GTP-dependent dimerization of G12X K-Ras variants using ultraviolet photodissociation mass spectrometry.

Authors:  M Rachel Mehaffey; Christopher L Schardon; Elisa T Novelli; Michael B Cammarata; Lauren J Webb; Walter Fast; Jennifer S Brodbelt
Journal:  Chem Sci       Date:  2019-07-15       Impact factor: 9.825

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