VisioProt-MS: interactive 2D maps from intact protein mass spectrometry

Abstract

Supplementary data are available at Bioinformatics online.

Top-Down and Intact Protein Mass Spectrometry Data Visualization for Proteoform Analysis Using VisioProt-MS

“…Alternatively, it can be adapted and included in more complex workflows. All the information concerning its features, compatibility, and usages can be found in Locard-Paulet et al 17 and on the associated online help (https://masstools.ipbs.fr/visioprothelp.html).…”

“…For MS traces, raw files were automatically deconvoluted with the rolling window deconvolution software RoWinPro 8 and the proteoform footprints were visualized with VisioProt-MS v2.0. 17 Top-down raw data were analyzed with Proteome Discoverer v2.2 (Thermo Scientific) using the ProSight PD Top-Down Low/High node. Briefly, intact protein spectra were deconvoluted with ReSpect (precursor mass between 20 000 and 30 000 Da and 100 ppm mass tolerance, charge state range between 15 and 35).…”

“…In addition, directly comparing these maps reveals differences in proteoform footprints between samples and/or experimental conditions. 1,8,[12][13][14][15][16] Recently, we developed a free standalone tool to facilitate this analytical step: VisioProt-MS. 17 Here, we will illustrate its use through the analysis of the 20S core particle of the human proteasome.…”

Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry

“…In a recently published study, a new standalone soware called VisioProt-MS was reported, which provides a 2D LC-MS map representation by taking-up LC-MS data of TD studies. 256 Further, VisioProt-MS can take-up data from different types of instrument congurations, e.g., FT-ICR, orbitrap, Q-TOF and therefore, aids in better comparison of the TD LC-MS data. The charge state of the precursor ion as well as of the fragment ions can be determined from the respective isotope peak m/z values, for which high-resolution mass analyzer is essential; in other words, MS/MS spectral data acquisitions must be accomplished in a high-resolution mass analyzer.…”

ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment

“…Ultimately, combining these approaches results in improved confidence in the identification (Ntai et al, 2016). Although there are tools capable of visualizing TDP data, such as VisioProt-MS, which is able to visualize plots of molecular weights of eluting proteins as a function of their retention time (Locard-Paulet et al, 2019;Lesne et al, 2019), there are very few computational tools that combine data from these different strategies. For instance, Proteome Discoverer enables to perform BUP and TDP database searches independently, but does not provide modules to check the number of identified peptides corresponding to an identified proteoform (Scheffler).…”