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A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra
2016
Bioinformatics
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We developed TopMG, a mass graphbased software tool for proteoform identification by top-down mass spectrometry. ...
Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. ...
The research was supported by the National Institute of General Medical Sciences, National Institutes of Health (NIH) through Grant R01GM118470. Conflict of Interest: none declared. ...
doi:10.1093/bioinformatics/btw806
pmid:28453668
pmcid:PMC5860502
fatcat:qzm46do25repfaywt76zpkron4
A graph-based approach for proteoform identification and quantification using top-down homogeneous multiplexed tandem mass spectra
2018
BMC Bioinformatics
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of proteoforms using top-down HomMTM spectra. ...
Results: We formulate the top-down HomMTM spectral identification problem as the minimum error k-splittable flow problem on graphs and propose a graph-based algorithm for the identification and quantification ...
Proteoform identification All top-down tandem mass spectra were deconvoluted using MS-Deconv [22] . ...
doi:10.1186/s12859-018-2273-4
pmid:30367573
fatcat:wh7iarat4ngejpnc2gw45ohhwa
Identification of Ultramodified Proteins Using Top-Down Tandem Mass Spectra
2013
Journal of Proteome Research
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However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify ...
We demonstrate that MS-Align-E identifies many proteoforms of histone H4 and benchmark it against the currently accepted software tools. ...
PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO1830. We thank Dr. David Stenoien for providing the core histone mixtures. ...
doi:10.1021/pr400849y
pmid:24188097
pmcid:PMC3905687
fatcat:adw5rjolovdlpa7ixqtptmoyie
A Markov Chain Monte Carlo Method for Estimating the Statistical Significance of Proteoform Identifications by Top-Down Mass Spectrometry
2019
Journal of Proteome Research
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Top-down mass spectrometry is capable of identifying whole proteoform sequences with multiple post-translational modifications because it generates tandem mass spectra directly from intact proteoforms. ...
However, most existing methods are designed for proteoform identifications without modifications, and the challenge remains for accurately estimating the statistical significance of proteoform identifications ...
Acknowledgement The research was supported by the National Institute of General Medical Sciences, National Institutes of Health (NIH) through Grants R01GM118470 and R01GM125991. ...
doi:10.1021/acs.jproteome.8b00562
pmid:30638379
pmcid:PMC6484843
fatcat:dehh63zdkzfhvpsjqalsdwjyna
MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics
2015
Molecular & Cellular Proteomics
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However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. ...
Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational ...
Guardado-Alvarez, and Yutong Jin for helpful discussions and Nicole Lane for critical reading of this manuscript. ...
doi:10.1074/mcp.o115.054387
pmid:26598644
pmcid:PMC4739683
fatcat:badyj7ppdfb7rkye2vgqqqezlm
A spectrum graph-based protein sequence filtering algorithm for proteoform identification by top-down mass spectrometry
2017
2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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Database search is the main approach for identifying proteoforms using top-down tandem mass spectra. ...
In this paper, we propose a novel filtering algorithm, which generates spectrum graphs from subspectra of the query spectrum and searches them against the protein database to find good candidates. ...
Acknowledgments The research was supported by the National Institute of General Medical Sciences, National Institutes of Health (NIH) through Grant R01GM118470, and the National Natural Science Foundation ...
doi:10.1109/bibm.2017.8217653
pmid:29503761
pmcid:PMC5831147
dblp:conf/bibm/YangZKBNWL17
fatcat:466oebiyybay3cenu577qscwtm
Mass graphs and their applications in top-down proteomics
[article]
2015
bioRxiv
pre-print
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In addition, we design mass graph alignment algorithms for proteoform identification by top-down mass spectrometry. ...
Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a "bird view" of intact proteoforms. ...
Spectral mass graphs Mass graphs are also used to represent top-down MS/MS spectra. ...
doi:10.1101/031997
fatcat:uw3uemlg75defftssou2hszwxy
Systematic Evaluation of Protein Sequence Filtering Algorithms for Proteoform Identification Using Top-Down Mass Spectrometry
2018
Proteomics
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Top-down mass spectrometry is commonly used for analyzing complex proteoforms because it provides whole sequence information of the proteoforms. ...
In this study, we present new protein sequence filtering algorithms that outperform existing ones for top-down mass spectrometry-based proteoform identification. ...
Acknowledgement The research was supported by the National Institute of General Medical Sciences, National Institutes of Health (NIH) through Grant R01GM118470. ...
doi:10.1002/pmic.201700306
pmid:29327814
fatcat:yultd5ei7vaidgkpqiilpxsuea
Top-Down Proteomics: Ready for Prime Time?
2017
Analytical Chemistry
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SAMPLE PREPARATION STRATEGIES Often overlooked, sample preparation remains one of the most important and challenging aspects in top-down proteomics. ...
(Figure 2a-b) . 69 By employing a two-dimensional sSEC-RPC approach, more than 4000 unique proteoforms were detected with a 15-fold increase of the proteins above 60 kDa, which greatly outperformed one-dimensional ...
The authors also thank Ruixiang Sun, and Zhijie Wu for helpful discussions, and ...
doi:10.1021/acs.analchem.7b04747
pmid:29161012
pmcid:PMC6138622
fatcat:gq2bxvzsojgwbdvvmll7inhwb4
A graph-based filtering method for top-down mass spectral identification
2018
BMC Genomics
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Database search has been the main approach for proteoform identification by top-down tandem mass spectrometry. ...
Results: In this paper, we propose a spectrum graph matching (SGM) based protein sequence filtering method for top-down mass spectral identification. ...
Availability of data and materials The data sets used in this paper are available at Massive (http://massive.ucsd. edu) with identification numbers MSV000082061 and MSV000082064. ...
doi:10.1186/s12864-018-5026-x
fatcat:uwgz5h2umjcdfomge52k6hqnky
Label-Free Relative Quantitation of Isobaric and Isomeric Human Histone H2A and H2B Variants by Fourier Transform Ion Cyclotron Resonance Top-Down MS/MS
2016
Journal of Proteome Research
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For many, the only tractable approach is with intact protein top-down tandem mass spectrometry. ...
The top-down MS/MS approach provides a path forward for more extensive elucidation of the biological role of many previously unstudied histone variants and post-translational modifications. ...
Acknowledgments This work was supported by NSF Division of Materials Research through DMR-06-54118, NIH General Medical Sciences through P01GM85354, and the State of Florida. ...
doi:10.1021/acs.jproteome.6b00414
pmid:27431976
pmcid:PMC6261780
fatcat:pb7mjuwcqvhdbmbp2pgrligfau
The null hypothesis of GSEA, and a novel statistical model for competitive gene set analysis
2017
Bioinformatics
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A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra Q. ...
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1354 Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies O.Nikolova, R.Moser, C.Kemp ...
doi:10.1093/bioinformatics/btw803
pmid:28453686
fatcat:sb6fgwb5ljhzrgobzz3wureyn4
Proteomics in heart failure: top-down or bottom-up?
2014
Pflügers Archiv: European Journal of Physiology
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In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and the analysis of posttranslational modifications, as well as ...
Two MS-based proteomics strategies exist: peptide-based bottomup and protein-based top-down proteomics-each with its own unique strengths and weaknesses for interrogating the proteome. ...
ZG would like to thank the National Institute of Health training grant T32GM008688. ...
doi:10.1007/s00424-014-1471-9
pmid:24619480
pmcid:PMC4037365
fatcat:4bacbqnbjvhojnurmdzpxo6v6m
Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity
2016
Nature Communications
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Furthermore, using various sources of erythropoietin we define and demonstrate the usage of a biosimilarity score to quantitatively assess structural similarity, which would also be beneficial for profiling ...
Here, we present an integrative approach, combining two advanced mass spectrometry-based methods, high-resolution native mass spectrometry and middle-down proteomics, to analyse this micro-heterogeneity ...
V.F. and A.J.R.H. acknowledge further support by the NWO TOP-Punt Grant 718.015.003. ...
doi:10.1038/ncomms13397
pmid:27824045
pmcid:PMC5105167
fatcat:wysz5u7f4razbnhtuvukvfhfle
Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome
2018
Molecular & Cellular Proteomics
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Top-down mass spectrometry (MS)-based proteomics has emerged as the most powerful method for characterization and quantification of protein modifications. ...
Herein, we have developed a straightforward and robust top-down liquid chromatography (LC)/MS-based targeted proteomics platform for simultaneous quantification of protein expression and PTMs with high ...
Acknowledgments-We thank Bifan Chen for critical reading of this manuscript. We also thank Matt Willetts, Vladimir Ondruska from Bruker and Cory Scanlan from Waters for the technical assistances. ...
doi:10.1074/mcp.tir118.001086
pmid:30591534
pmcid:PMC6398208
fatcat:sv3tjfp5vrdcppj7emq5e6l5cu
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