VEMS 3.0:  Algorithms and Computational Tools for Tandem Mass Spectrometry Based Identification of Post-translational Modifications in Proteins

2005 ◽  
Vol 4 (6) ◽  
pp. 2338-2347 ◽  
Author(s):  
Rune Matthiesen ◽  
Morten Beck Trelle ◽  
Peter Højrup ◽  
Jakob Bunkenborg ◽  
Ole N. Jensen
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Computational Tools ◽  
Post Translational Modifications

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 Analysis of Monoclonal Antibody Sequence and Post-translational Modifications by Time-controlled Proteolysis and Tandem Mass Spectrometry

2015 ◽  
Vol 15 (4) ◽  
pp. 1479-1488 ◽  
Author(s):  
Lichao Zhang ◽  
A. Michelle English ◽  
Dina L. Bai ◽  
Scott A. Ugrin ◽  
Jeffrey Shabanowitz ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Monoclonal Antibody ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Post Translational Modifications ◽  
Antibody Sequence

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 Computational refinement of post-translational modifications predicted from tandem mass spectrometry

2011 ◽  
Vol 27 (6) ◽  
pp. 797-806 ◽  
Author(s):  
Clement Chung ◽  
Jian Liu ◽  
Andrew Emili ◽  
Brendan J. Frey
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Tandem Mass ◽  
Post Translational Modifications

scholarly journals Mapping post‐translational modifications of the histone variant macroH2A1 using tandem mass spectrometry

2006 ◽  
Vol 20 (4) ◽  
Author(s):  
Feixia Chu ◽  
Dmitri A Nusinow ◽  
Robert J Chalkley ◽  
Kathrin Plath ◽  
Barbara Panning ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Histone Variant ◽  
Tandem Mass ◽  
Post Translational Modifications

scholarly journals Locally different proteome in aortas from patients with stenotic tricuspid and bicuspid aortic valves†

2019 ◽  
Vol 56 (3) ◽  
pp. 458-469 ◽  
Author(s):  
Amalia Forte ◽  
Xiaoke Yin ◽  
Marika Fava ◽  
Ciro Bancone ◽  
Marilena Cipollaro ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Tandem Mass Spectrometry ◽  
Cellular Protein ◽  
Tandem Mass ◽  
Differential Proteomics ◽  
Aortic Valves ◽  
Post Translational Modifications ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass

Abstract OBJECTIVES We aimed to compare the intracellular proteome of ascending aortas from patients with stenotic bicuspid (BAV) and tricuspid aortic valves (TAV) to identify BAV-specific pathogenetic mechanisms of aortopathy and to verify the previously reported asymmetric expression of BAV aortopathy [concentrated at the convexity (CVX)] in its ‘ascending phenotype’ form. METHODS Samples were collected from the CVX and concavity sides of non-aneurysmal ascending aortas in 26 TAV and 26 BAV patients undergoing stenotic aortic valve replacement. Aortic lysates were subjected to cellular protein enrichment by subfractionation, and to proteome comparison by 2-dimensional fluorescence difference in-gel electrophoresis. Differentially regulated protein spots were identified by liquid chromatography–tandem mass spectrometry and analysed in silico. Selected results were verified by immunofluorescence and reverse transcription-polymerase chain reaction. RESULTS In BAV samples, 52 protein spots were differentially regulated versus TAV samples at the CVX and 10 spots at the concavity: liquid chromatography–tandem mass spectrometry identified 35 and 10 differentially regulated proteins, respectively. Charge trains of individual proteins (e.g. annexins) suggested the presence of post-translational modifications possibly modulating their activity. At the CVX, 37 of the 52 different protein spots showed decreased expression in BAV versus TAV. The affected biological pathways included those involved in smooth muscle cell contractile phenotype, metabolism and cell stress. CONCLUSIONS The observed differential proteomics profiles may have a significant impact on the pathogenesis of the aortopathy, pointing the way for further studies. At a preaneurysmal stage, an aorta with BAV shows more protein expression changes and potentially more post-translational modifications at the CVX of the ascending aorta than at the concavity, compared to that of TAV.

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