scholarly journals Using TDFragMapper: a high-performance tool to assess experimental parameters in top-down proteomics

2021 ◽  
Author(s):  
Diogo Borges Lima ◽  
Jonathan Dhenin ◽  
Mathieu Dupré ◽  
Julia Chamot-Rooke
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Software Tool ◽  
Intact Protein ◽  
Tandem Mass ◽  
Top Down ◽  
Experimental Conditions ◽  
Intact Proteins ◽  
Fragment Ions ◽  
Experimental Parameters

Abstract Here we present a new software-tool for visualizing fragment ions and sequence coverage of intact proteins in top-down mass spectrometry. TDFragMapper combines the data arising from multiple and diverse tandem mass spectrometry experiments of intact proteins. Our tool maps fragment ions onto the protein backbone sequence and allows for a rapid comparison of the results obtained when varying experimental parameters in tandem mass spectrometry (MS/MS) experiments of intact proteins: fragmentation method, selected precursor charge state, activation level, technical replicate. In summary, TDFragMapper is a unique software-tool that allows an easy selection of the best experimental conditions leading to the highest confidence in intact protein sequence identification.

scholarly journals TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics

2021 ◽  
Author(s):  
Jonathan Steven Dhenin ◽  
Diogo Borges Lima ◽  
Mathieu Dupre ◽  
Julia Chamot-Rooke
Keyword(s):  
Software Tool ◽  
Rapid Evaluation ◽  
Visualization Tool ◽  
Sequence Coverage ◽  
Top Down ◽  
Intact Proteins ◽  
Fragment Ions ◽  
Experimental Parameters ◽  
Demonstration Video

We present a new software-tool allowing an easy visualization of fragment ions and thus a rapid evaluation of key experimental parameters on the sequence coverage obtained for the MS/MS analysis of intact proteins. Our tool can deal with multiple fragmentation methods. We demonstrate that TDFragMapper can rapidly highlight the experimental fragmentation parameters that are critical to the characterization of intact proteins of various size using top-down proteomics. TDFragMapper, a demonstration video and user tutorial are freely available at https://msbio.pasteur.fr/tdfragmapper, for academic use; all data are thus available from the ProteomeXchange consorti-um (identifier PXD024643).

scholarly journals Top-down proteomic identification of plasmid and host proteins produced by pathogenic Escherichia coli using MALDI-TOF-TOF tandem mass spectrometry

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0260650
Author(s):  
Clifton K. Fagerquist ◽  
Claire E. Dodd
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Tandem Mass Spectrometry ◽  
Aspartic Acid ◽  
Protein Sequences ◽  
Tandem Mass ◽  
Host Proteins ◽  
Top Down ◽  
Maldi Tof ◽  
Fragment Ions

Fourteen proteins produced by three pathogenic Escherichia coli strains were identified using antibiotic induction, MALDI-TOF-TOF tandem mass spectrometry (MS/MS) and top-down proteomic analysis using software developed in-house. Host proteins as well as plasmid proteins were identified. Mature, intact protein ions were fragmented by post-source decay (PSD), and prominent fragment ions resulted from the aspartic acid effect fragmentation mechanism wherein polypeptide backbone cleavage (PBC) occurs on the C-terminal side of aspartic acid (D), glutamic acid (E) and asparagine (N) residues. These highly specific MS/MS-PSD fragment ions were compared to b- and y-type fragment ions on the C-terminal side of D-, E- and N-residues of in silico protein sequences derived from whole genome sequencing. Nine proteins were found to be post-translationally modified with either removal of an N-terminal methionine or a signal peptide. The protein sequence truncation algorithm of our software correctly identified all full and truncated protein sequences. Truncated sequences were compared to those predicted by SignalP. Nearly complete concurrence was obtained except for one protein where SignalP mis-identified the cleavage site by one residue. Two proteins had intramolecular disulfide bonds that were inferred by the absence of PBC on the C-terminal side of a D-residue located within the disulfide loop. These results demonstrate the utility of MALDI-TOF-TOF for identification of full and truncated bacterial proteins.

Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Tandem Mass Spectrometry ◽  
Mass Spectra ◽  
Protein Modification ◽  
Software Tool ◽  
Tandem Mass ◽  
Simulation Data ◽  
Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

scholarly journals Nano-LC FTICR Tandem Mass Spectrometry for Top-Down Proteomics: Routine Baseline Unit Mass Resolution of Whole Cell Lysate Proteins up to 72 kDa

2012 ◽  
Vol 84 (5) ◽  
pp. 2111-2117 ◽  
Author(s):  
Jeremiah D. Tipton ◽  
John C. Tran ◽  
Adam D. Catherman ◽  
Dorothy R. Ahlf ◽  
Kenneth R. Durbin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Mass Resolution ◽  
Unit Mass ◽  
Tandem Mass ◽  
Top Down ◽  
Whole Cell ◽  
Whole Cell Lysate ◽  
Cell Lysate ◽  
Unit Mass Resolution

scholarly journals A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome

2009 ◽  
Vol 20 (12) ◽  
pp. 2183-2191 ◽  
Author(s):  
Ji Eun Lee ◽  
John F. Kellie ◽  
John C. Tran ◽  
Jeremiah D. Tipton ◽  
Adam D. Catherman ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Two Dimensional ◽  
Top Down ◽  
Low Mass
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