Publications

MASH Software Publications

• Larson, E.J. ; Pergande, M. R; Moss, M. E.; Rossler, K. J.; Wenger, R. K.; Krichel, B.; Josyer, H.; Melby, J. A.; Roberts, D. S.; Pike, K.; Shi, Z.; Chan, H.; Knight, B.; Rogers, H. T.; Brown, K. A.; Ong, I. M.; Kyowon Jeong, K.; Marty, M.; McIlwain, S. J.; Ge, Y. MASH Native: A Unified Solution for Native Top-Down Proteomics Data Processing Bioinformatics, 2023, btad359, Link
  
  
  
• Wu, Z.; Roberts, D.S.; Melby, J.A.; Wenger, K.; Wetzel, M.; Gu, Y.; Ramanathan, S.G.; Bayne, E.F.; Liu, X.; Sun, R.; Ong, I.M.; McIlwain, S.J.; Ge, Y. MASH Explorer: A Universal Software Environment for Top-Down Proteomics., J. Proteome Res., 2020, 19 (9), 3867-3876. Link
• S. J. McIlwain, Z. Wu, M. Wetzel, D. Belongia, Y. Jin, K. Wenger, I. Ong, Y. Ge, Enhancing Top-down Proteomics Data Analysis by Combining Deconvolution Results through a Machine Learning Strategy, Journal of the American Society for Mass Spectrometry, 2020, 31, 5, 1104-1113. Link
• W. Cai, H. Guner, Z. R. Gregorich, A. J. Chen, S. Ayaz-Guner, Y. Peng, S. G. Valeja, X. Liu, Y. Ge. MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics. Molecular & Cellular Proteomics, 2016, 15, 703-714. Link
• H. Guner, P. L. Close, W. Cai, H. Zhang, Y. Peng, Z. R. Gregorich, Y. Ge. MASH Suite: A User-Friendly and Versatile Software Interface for High-Resolution Mass Spectrometry Data Interpretation and Visualization. Journal of the American Society for Mass Spectrometry, 2014, 25, 464-470. Link


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• Click here for the citation list of MASH Suite Pro
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Representative Publications Citing MASH Software

• J. A. Melby, Y. Jin, Z. Lin, T. Tucholski, Z. Wu, Z. R. Gregorich, G. M. Diffee, Y. Ge. Top-Down Proteomics Reveals Myofilament Proteoform Heterogeneity among Various Rat Skeletal Muscle Tissues, Journal of Proteome Research, 2020, 19, 446-454. Link
• K. Jeong, J. Kim, M. Gaikwad, S. N. Hidayah, L. Heikaus, H. Schluter, O. Kohlbacher, FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics, Cell Systems, 2020, 10, 213-218. Link
• R. Bacala, B. Fu, H. Perreault, D. W. Hatcher, Quantitative LC-MS intact proteoform profiling of wheat glutenin subunits, Journal of Cereal Science, 2020. Link
• J. Zhong, Y. Sun, M. Xie, W. Peng, C. Zhang, F. Wu, J. Wang, Proteoform characterization based on top-down mass spectrometry, Briefings in Bioinformatics, 2020. Link
• M. Zhou, N. Malhan, A. H. Ahkami, K. Engbrecht, G. Myers, J. Dahlberg, J. Hollingswoth, J. A. Sievert, R. Hutmacher, M. Madera, P. G. Lemaux, K. K. Hixson, C. Jansson, L. Pasa-Tolic. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation, Methods, 2019. Link
• D. S. Roberts, B. Chen, T. N. Tiambeng, Z. Wu, Y. Ge, S. Jin. Reproducible large-scale synthesis of surface silanized nanoparticles as an enabling nanoproteomics platform: Enrichment of the human heart phosphoproteome, Nano Research, 2019, 12, 1473-1481 Link
• B. Chen, Z. Lin, Y. Zhu, Y. Jin, E. Larson, Q. Xu, C. Fu, Z. Zhang, Q. Zhang, W. A. Pritts, Y. Ge. Middle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation, Analytical Chemistry, 2019, 12, 1473-1481 Link
• V. Bortnov, M. Tonelli, W. Lee, Z. Lin, D. S. Annis, O. N. Demerdash, A. Bateman, J. C. Mitchell, Y. Ge, J. L. Markley, D. F. Mosher. Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum, Nature Communications, 2019, 10, 5612. Link
• K. A. Brown, B. Chen, T. M. Guardado-Alvarez, Z. Lin, L. Hwang, S. Ayaz-Guner, S. Jin, Y. Ge. A photocleavable surfactant for top-down proteomics. Nature Methods, 2019, 16, 417-420. Link
• L. V. Schaffer, R. J. Millikin, R. M. Miller, L. C. Anderson, R. T. Fellers, Y. Ge, N. L. Kelleher, R. D. LeDuc, X. Liu, S. H. Payne, L. Sun, P. M. Thomas, T. Tucholski, Z. Wang, S. Wu, Z. Wu, D. Yu, M. R. Shortread, L. M. Smith. Identification and Quantification of Proteoforms by Mass Spectrometry. Proteomics, 2019, 19, 1800361. Link
• K. Srzentic, K. O. Nagornov, L. Fornelli, A. A. Lobas, D. Ayoub, A. N. Kozhinov, N. Gasilova, L. Menin, A. Beck, M. V. Gorshkov, K. Aizikov, Y. O. Tsybin. Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody. Analytical Chemistry, 2018, 90, 21, 12527-12535. Link
• F. Gomes, B. Lemma, D. Abeykoon, D. Chen, Y. Wang, D. Fushman, C. Fenselau. Top‐down analysis of novel synthetic branched proteins. Journal of Mass Spectrometry, 2018, 54, 19-25. Link
• G. Xu, J. Stupak, L. Yang, L. Hu, B. Guo, J. Li. Deconvolution in mass spectrometry based proteomics. Rapid Communications in Mass Spectrometry, 2018, 32, 763-774. Link
• D. F. Smelter, W. J. de Lange, W. Cai, Y. Ge, J. C. Ralphe. The HCM-linked W792R mutation in cardiac myosin-binding protein C reduces C6 FnIII domain stability. American Journal of Physiology Heart and Circulatory Physiology, 2018, 314, H1179-H1191. Link
• H. Chang, C. Chen, C. Ko, Y. Chen, Y. Chen, W. Hsu, C. Juo, T. Sung. iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm. Analytical Chemistry, 2017, 89, 24, 13128-13136. Link
• A. S. J. B. Rana, Y. Ge, E. R. Strieter. Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry (UbiChEM-MS) Reveals Cell-Cycle Dependent Formation of Lys11/Lys48 Branched Ubiquitin Chains. Journal of Proteome Research, 2017, 16, 9, 3363-3369. Link
• C-G, Wu, H. Chen, F. Guo, V. K. Yadav, S. J. McIlwain, M. Rowse, A. Choudhary, Z. Lin, Y. Li, T. Gu, A, Zheng, Q. Xu, W. Lee, E. Resch, B. Johnson, J. Day, Y. Ge, I. M. Ong, M. E. Burkard, Y. Ivarsson, Y. Xing. PP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis. Cell Discovery, 2017, 3, 17027. Link
• W. Cai, Z.L. Hite, B. Lyu, Z. Lin, Z. R. Gregorich, A. E. Messer, S. J. McIlwain, S. B. Marston, T. Kohmoto, Y. Ge. Temperature-sensitive sarcomeric protein post-translational modifications revealed by top-down proteomics. Journal of Molecular and Cellular Cardiology, 2018, 122, 11-22. Link
• J. Park, P.D. Piehowski, C. Wilkins, A. Zhou, J. Mendoza, G. M. Fujimoto, B. C. Gibbons, J. B. Shaw, Y. Shen, A. K. Shukla, R. J. Moore, T. liu, V. A. Petyuk, N. Tolic, L. Pasa-Tolic, R. D. Smith, S. H. Payne, S. Kim. Informed-Proteomics: open-source software package for top-down proteomics. Nature Methods, 2017, 14, 909-914. Link
• J. J. Calvete, D. Petras, F. Calderon-Celis, B. Lemonte, J. Ruiz Encinar, A. Sanz-Medel. Protein-species quantitative venomics: looking through a crystal ball. Journal of Venomous Animals and Toxins including Tropical Disease, 2017, 23: 27. Link
• D. Yu, Y. Peng, S. Ayaz-Guner, Z. R. Gregorich, Y. Ge. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry. Journal of The American Society for Mass Spectrometry, 2016, 27, 220-232. Link
• B. Q. Tran, C. Barton, J. Feng, A. Sandjong, S. H. Yoon, S. Awasthi, T. Liang, M. M. Khan, D. P. A. Kilgour, D. R. Goodlett, Y. A. Goo. Glycosylation characterization of therapeutic mAbs by top- and middle-down mass spectrometry. Data in Brief, 2016, 6, 68-76. Link
• B. Q. Tran, C. Barton, J. Feng, A. Sandjong, S. H. Yoon, S. Awasthi, T. Liang, M. M. Khan, D. P. A. Kilgour, D. R. Goodlett, Y. A. Goo. Comprehensive glycosylation profiling of IgG and IgG-fusion proteins by top-down MS with multiple fragmentation techniques. Journal of Proteomics, 2016, 134, 93-101. Link
• A. C. Susa, Z. Xia, H. Y. H. Tang, J. A. Tainer, E. R. Williams. Charging of Proteins in Native Mass Spectrometry. Journal of The American Society for Mass Spectrometry, 2016, 1-9. Link
• A. Serra, X. Gallart-Palau, R. S.-E. See-Toh, X. Hemu, J. P. Tam, S. K. Sze. Commercial processed soy-based food product contains glycated and glycoxidated lunasin proteoforms. Scientific Reports, 2016, 6, 26106. Link
• Y. Jin, Y. Peng, Z. Lin, Y.-C. Chen, L. Wei, T. A. Hacker, L. Larsson, Y. Ge. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. Journal of Muscle Research and Cell Motility, 2016, 37, 41-52. Link
• S. G. Valeja, L. Xiu, Z. R. Gregorich, H. Guner, S. Jin, Y. Ge. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Analytical Chemistry, 2015, 87, 5363-5371. Link
• R. C. Molden, N. V. Bhanu, G. LeRoy, A. M. Arnaudo, B. A. Garcia. Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications. Epigenetics & Chromatin, 2015, 8, 15. Link
• F. Lermyte, M. K. Łącki, D. Valkenborg, G. Baggerman, A. Gambin, F. Sobott. Understanding reaction pathways in top-down ETD by dissecting isotope distributions: A mammoth task. International Journal of Mass Spectrometry, 2015, 390, 146-154. Link
• Z. R. Gregorich, Y. Peng, N. M. Lane, J. J. Wolff, S. Wang, W. Guo, H. Guner, J. Doop, T. A. Hacker, Y. Ge. Comprehensive assessment of chamber-specific and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. Journal of Molecular and Cellular Cardiology, 2015, 87, 102-112. Link
• Y.-C. Chen, S. Ayaz-Guner, Y. Peng, N. M. Lane, M. R. Locher, T. Kohmoto, L. Larsson, R. L. Moss, Y. Ge. Effective top-down LC/MS+ method for assessing actin isoforms as a potential cardiac disease marker. Analytical Chemistry 2015, 87, 8399-8406. Link
• L. Xiu, S. G. Valeja, A. J. Alpert, S. Jin, Y. Ge, Analytical Chemistry, 2014, 86, 7899-7906. Link
• E. M. Valkevich, N. A. Sanchez, Y. Ge, E. R. Strieter. Middle-down mass spectrometry enables characterization of branched ubiquitin chains. Biochemistry, 2014, 53, 4979-4989. Link
• Y. Peng, Z. R. Gregorich, S. G. Valeja, H. Zhang, W. Cai, Y.-C. Chen, H. Guner, A. J. Chen, D. J. Schwahn, T. A. Hacker, X. Liu, Y. Ge. Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction. Molecular & Cellular Proteomics, 2014, 13, 2752-2764. Link
• Y. Peng, S. Ayaz-Guner, D. Yu, Y. Ge. Top-down mass spectrometry of cardiac myofilament proteins in health and disease. PROTEOMICS – Clinical Applications, 2014, 8, 554-568. Link
• R. C. Molden, B. A. Garcia. Middle-Down and Top-Down Mass Spectrometric Analysis of Co-occurring Histone Modifications. Current Protocols in Protein Science, John Wiley & Sons, Inc., 2014. Link
• Z. R. Gregorich, Y. Ge. Top-down proteomics in health and disease: challenges and opportunities. PROTEOMICS, 2014, 14, 1195-1210. Link