MASH Explorer

Links

DeconEngine

N. Jaitly, A. Mayampurath, K. Littlefield, J. N. Adkins, G. A. Anderson, and R. D. Smith. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics, 2009, 10: 87. Link

Informed Proteomics

J. Park, P. D. Piehowski, C. Wilkins, M. 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, and S. Kim. Informed-Proteomics: Open Source Software Package for Top-down Proteomics. Nature Methods, 2017, 14: 9. 909-914. Link

MS-Align+

X. Liu, Y. Sirotkin, Y. Shen, G. Anderson, Y. S. Tsai, Y. S. Ting, D. R. Goodlett, R. D. Smith, V. Bafna, and P. A. Pevzner. Protein Identification Using Top-Down Spectra. Molecular & Cellular Proteomics, 2012, 11: 6 Link

Ms-Deconv

X. Liu, Y. Inbar, P. C. Dorrestein, C. Wynne, N. Edwards, P.Souda, J. P. Whitelegge, V. Bafna, and P. A. Pevzner. Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins. Molecular & Cellular Proteomics , 2010, 9, 12: 2772-2782. Link

pParseTD

Z.-F. Yuan, C. Liu, H.-P. Wang, R.-X. Sun, Y. Fu, J.-F. Zhang, L.-H. Wang, H. Chi, Y. Li, L.-Y. Xiu, W.-P. Wang, S.-M. He. pParse: a method for accurate determination of monoisotopic peaks in high-resolution mass spectra. Proteomics , 2012, 12: 2, 226–235, Link

ProteoWizard

M.C. Chambers, B. MacLean, R. Burke, D. Amode, D.L. Ruderman, S. Neumann, L. Gatto, B. Fischer, B.Pratt, J. Egertson, K. Hoff, D. Kessner, N. Tasman, N. Shulman, B. Frewen, T.A. Baker, M.-Y. Brusniak, C. Paulse, D. Creasy, L. Flashner,K. Kani, C. Moulding, S. L.Seymour, L. M. Nuwaysir, B. Lefebvre, F. Kuhlmann, J. Roark, P. Rainer, S. Detlev, T. Hemenway, A. Huhmer, J. Langridge, B. Connolly, T. Chadick, K. Holly, J. Eckels, E. W. Deutsch, R. L. Moritz, J. E. Katz, D. B. Agus, M. MacCoss, D. L. Tabb, & P. Mallick. A cross-platform toolkit for mass spectrometry and proteomics. Nature Biotechnology, 2012, 30, 918-920. Link

pTOP

pTop 1.0: a High-accuracy and High-efficiency Search Engine for Intact Protein Identification. R.-X. Sun, L. Luo, L. Wu, R.-M. Wang, W.-F. Zeng, H. Chi, C. Liu, and S.-M. He. Analytical Chemistry, 2016, 88, 3082-3090. Link

THRASH

D. M. Horn, R. A. Zubarev, and F. W. McLafferty. Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules, Journal of the American Society for Mass Spectrometry, 2000, 11: 4, 320-332, Link

TopPIC

Q. Kou, L. Xun, and X. Liu. TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. Bioinformatics, 2016, 32 , 3495-3497. Link

FLASHDeconv

K. Jeong, J. Kim, M. Gaikwad, S. N. Hidayah, L. Heikaus, H. Schlüter, and O. Kohlbacher, FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics. Cell Systems, 2020, 10, 213-218. Link

UniDec Series

M. T. Marty , A. J. Baldwin , E. G. Marklund , G. K. A. Hochberg , J. L. P. Benesch , and C. V. Robinson."Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles" Analytical Chemistry, 2015, DOI: 10.1021/acs.analchem.5b00140.
D. J. Reid, J. M. Diesing, M. A. Miller, S. M. Perry, J. A. Wales, W. R. Montfort, M. T. Marty." MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra" Journal of the American Society for Mass Spectrometry, 2019, DOI: https://doi.org/10.1007/s13361-018-1951-9