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A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

Qiang Kou, Si Wu, Nikola Tolić, Ljiljana Paša-Tolić, Yunlong Liu, Xiaowen Liu
2016 Bioinformatics  
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

Kaiyuan Zhu, Xiaowen Liu
2018 BMC Bioinformatics  
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

Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolić, Ljiljana Pasa-Tolić, Pavel A. Pevzner
2013 Journal of Proteome Research  
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

Qiang Kou, Zhe Wang, Rachele A. Lubeckyj, Si Wu, Liangliang Sun, Xiaowen Liu
2019 Journal of Proteome Research  
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

Wenxuan Cai, Huseyin Guner, Zachery R. Gregorich, Albert J. Chen, Serife Ayaz-Guner, Ying Peng, Santosh G. Valeja, Xiaowen Liu, Ying Ge
2015 Molecular & Cellular Proteomics  
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

Runmin Yang, Daming Zhu, Qiang Kou, Poornima Bhat-Nakshatri, Harikrishna Nakshatri, Si Wu, Xiaowen Liu
2017 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
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]

Qiang Kou, Si Wu, Nikola Tolić, Ljiljana Pasa-Tolić, Xiaowen Liu
2015 bioRxiv   pre-print
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

Qiang Kou, Si Wu, Xiaowen Liu
2018 Proteomics  
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?

Bifan Chen, Kyle A. Brown, Ziqing Lin, Ying Ge
2017 Analytical Chemistry  
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

Runmin Yang, Daming Zhu
2018 BMC Genomics  
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

Xibei Dang, Amar Singh, Brian D. Spetman, Krystal D. Nolan, Jennifer S. Isaacs, Jonathan H. Dennis, Stephen Dalton, Alan G. Marshall, Nicolas L. Young
2016 Journal of Proteome Research  
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

Birgit Debrabant
2017 Bioinformatics  
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?

Zachery R. Gregorich, Ying-Hua Chang, Ying Ge
2014 Pflügers Archiv: European Journal of Physiology  
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

Yang Yang, Fan Liu, Vojtech Franc, Liem Andhyk Halim, Huub Schellekens, Albert J. R. Heck
2016 Nature Communications  
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

Ziqing Lin, Liming Wei, Wenxuan Cai, Yanlong Zhu, Trisha Tucholski, Stanford D. Mitchell, Wei Guo, Stephen P. Ford, Gary M. Diffee, Ying Ge
2018 Molecular & Cellular Proteomics  
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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