ProSight PTM 2.0: improved protein identification and characterization for top down mass spectrometry
Open accessAbstract
ProSight PTM 2.0 (http://prosightptm2.scs.uiuc.edu) is the next generation of the ProSight PTM web-based system for the identification and characterization of proteins using top down tandem mass spectrometry. It introduces an entirely new data-driven interface, integrated Sequence Gazer for protein characterization, support for fixed modifications, terminal modifications and improved support for multiple precursor ions (multiplexing). Furthermore, it supports data import and export for local analysis and collaboration.
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Complex-down data interpretation is similar to TDMS of denatured proteins; therefore, many existing software packages for TDMS can be retrofitted for complex-down data.
“Data interpretation for complex-down spectra is similar to TDMS of denatured proteins; therefore, many existing software packages for TDMS can be retrofitted for complex-down data, including ProSight PTM 2.0,115 ProSight Lite,116 MASH Suite,117–119 ProteinGoggle,120 TopPIC,121 Informed-Proteomics,122 Masstodon,123 and others.”
From Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry (2020) · cites this paper as [115]
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Cites
Proteomic analysis of post-translational modifications
Mann, M., & Jensen, O. N. (2003) · Nature Biotechnology · doi:10.1038/nbt0303-255 · Cited by 2,136 · see citing works
Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process
Zubarev, R. A., Kelleher, N. L., & McLafferty, F. W. (1998) · Journal of the American Chemical Society · doi:10.1021/ja973478k · Cited by 1,881 · see citing works
Self-citationPhosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F., & White, F. M. (2002) · Nature Biotechnology · doi:10.1038/nbt0302-301 · Cited by 1,636 · see citing works
Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags
Mann, M., & Wilm, M. S. (1994) · Analytical Chemistry · doi:10.1021/ac00096a002 · Cited by 1,473 · see citing works
Current Protocols in Bioinformatics
Korch, C. T. (2002) · John Wiley & Sons, Inc. eBooks · doi:10.1002/0471250953 · Cited by 1,226 · see citing works
dbSNP: a database of single nucleotide polymorphisms
Smigielski, E. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.352 · Cited by 623 · see citing works
Ion formation from charged droplets: Roles of geometry, energy, and time
Fenn, J. B. (1993) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(93)85014-o · Cited by 519 · see citing works
Automated reduction and interpretation of
Horn, D. M., Zubarev, R. A., & McLafferty, F. W. (2000) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(99)00157-9 · Cited by 507 · see citing works
Senko, M. W., Canterbury, J. D., Guan, S., & Marshall, A. G. (1996) · Rapid Communications in Mass Spectrometry · doi:10.1002/(sici)1097-0231(199611)10:14 · Cited by 256 · see citing works
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
Karchin, R., Diekhans, M., Kelly, L., Thomas, D. J., Pieper, U., Eswar, N., Haussler, D. H., & Šali, A. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti442 · Cited by 228 · see citing works
Informatics and multiplexing of intact protein identification in bacteria and the archaea
Meng, F., Cargile, B. J., Miller, L. M., Forbes, A. J., Johnson, J. R., & Kelleher, N. L. (2001) · Nature Biotechnology · doi:10.1038/nbt1001-952 · Cited by 210 · see citing works
Self-citationLeDuc, R. D., Taylor, G. K., Kim, Y.-B., Januszyk, T. E., Bynum, L., Solà, J., Garavelli, J., & Kelleher, N. (2004) · Nucleic Acids Res. · doi:10.1093/nar/gkh447 · Cited by 192 · see citing works
Self-citationApproaching complete peroxisome characterization by gas-phase fractionation
Yi, E. C., Marelli, M., Lee, H., Purvine, S. O., Aebersold, R. H., Aitchison, J. D., & Goodlett, D. R. (2002) · Electrophoresis · doi:10.1002/1522-2683(200209)23:18 · Cited by 183 · see citing works
Pesavento, J. J., Kim, Y.-B., Taylor, G. K., & Kelleher, N. L. (2004) · Journal of the American Chemical Society · doi:10.1021/ja039748i · Cited by 156 · see citing works
Self-citationAnalysis of the microbial proteome
Washburn, M. P., & Yates, J. R. (2000) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00092-8 · Cited by 142 · see citing works
Roth, M. J., Forbes, A. J., Boyne, M., Kim, Y.-B., Robinson, D., & Kelleher, N. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500064-mcp200 · Cited by 96 · see citing works
Self-citationGas-Phase Concentration, Purification, and Identification of Whole Proteins from Complex Mixtures
Reid, G. E., Shang, H., Hogan, J. M., Lee, G. U., & McLuckey, S. A. (2002) · Journal of the American Chemical Society · doi:10.1021/ja025966k · Cited by 95 · see citing works
New and automated MSn approaches for top-down identification of modified proteins
Zabrouskov, V., Senko, M. W., Du, Y., LeDuc, R. D., & Kelleher, N. L. (2005) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2005.08.004 · Cited by 76 · see citing works
Self-citationLeDuc, R. D., & Kelleher, N. L. (2007) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1306s19 · Cited by 42 · see citing works
Self-citationThe RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database
Garavelli, J. S. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.1.199 · Cited by 24 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Mapping intact protein isoforms in discovery mode using top-down proteomics
Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E., Catherman, A. D., Durbin, K. R., Tipton, J. D., Vellaichamy, A., Kellie, J. F., Li, M., et al. (2011) · Nature · doi:10.1038/nature10575 · Cited by 665 · see citing works
Self-citationTop Down proteomics: Facts and perspectives
Catherman, A. D., Skinner, O. S., & Kelleher, N. L. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.02.041 · Cited by 507 · see citing works
Self-citationKou, Q., Xun, L., & Liu, X. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw398 · Cited by 276 · see citing works
ProSight Lite: Graphical software to analyze top‐down mass spectrometry data
Fellers, R. T., Greer, J. B., Early, B. P., Yu, X., LeDuc, R. D., Kelleher, N. L., & Thomas, P. M. (2015) · PROTEOMICS · doi:10.1002/pmic.201400313 · Cited by 247 · see citing works
Self-citationTop‐down proteomics in health and disease: Challenges and opportunities
Gregorich, Z. R., & Ge, Y. (2014) · PROTEOMICS · doi:10.1002/pmic.201300432 · Cited by 217 · see citing works
Identification and Quantification of Proteoforms by Mass Spectrometry
Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., et al. (2019) · PROTEOMICS · doi:10.1002/pmic.201800361 · Cited by 209 · see citing works
Self-citationTop-Down Proteomics: Ready for Prime Time?
Chen, B., Brown, K. A., Lin, Z., & Ge, Y. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04747 · Cited by 210 · see citing works
Deconvolution and Database Search of Complex Tandem Mass Spectra of Intact Proteins
Liu, X., Inbar, Y., Dorrestein, P. C., Wynne, C., Edwards, N., Souda, P., Whitelegge, J. P., Bafna, V., & Pevzner, P. A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.002766 · Cited by 170 · see citing works
Panchaud, A., Affolter, M., & Kussmann, M. (2012) · Journal of Proteomics · doi:10.1016/j.jprot.2011.12.022 · Cited by 159 · see citing works
Protein Identification Using Top-Down Spectra
Liu, X., Sirotkin, Y., Shen, Y., Anderson, G., Tsai, Y. S., Ting, Y. S., Goodlett, D. R., Smith, R. D., Bafna, V., & Pevzner, P. A. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.008524 · Cited by 153 · see citing works
Zhou, M., Lantz, C., Brown, K. A., Ge, Y., Paša-Tolić, L., Loo, J. A., & Lermyte, F. (2020) · Chemical Science · doi:10.1039/d0sc04392c · Cited by 146 · see citing works
MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics
Cai, W., Guner, H., Gregorich, Z. R., Chen, A. J., Ayaz-Guner, S., Peng, Y., Valeja, S. G., Liu, X., & Ge, Y. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o115.054387 · Cited by 132 · see citing works
Top-down Proteomics: Technology Advancements and Applications to Heart Diseases
Cai, W., Tucholski, T. M., Gregorich, Z. R., & Ge, Y. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2016.1209414 · Cited by 99 · see citing works
Kellie, J. F., Tran, J. C., Lee, J. E., Ahlf, D. R., Thomas, H. M., Ntai, I., Catherman, A. D., Durbin, K. R., Zamdborg, L., Vellaichamy, A., et al. (2010) · Molecular BioSystems · doi:10.1039/c000896f · Cited by 99 · see citing works
Self-citationCleland, T. P., DeHart, C. J., Fellers, R. T., VanNispen, A. J., Greer, J. B., LeDuc, R. D., Parker, W. R., Thomas, P. M., Kelleher, N. L., & Brodbelt, J. S. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00043 · Cited by 96 · see citing works
Self-citationAnderson, L. C., DeHart, C. J., Kaiser, N. K., Fellers, R. T., Smith, D. F., Greer, J. B., LeDuc, R. D., Blakney, G. T., Thomas, P. M., Kelleher, N. L., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00696 · Cited by 94 · see citing works
Self-citationLeDuc, R. D., Fellers, R. T., Early, B. P., Greer, J. B., Thomas, P. M., & Kelleher, N. L. (2014) · Journal of Proteome Research · doi:10.1021/pr401277r · Cited by 85 · see citing works
Self-citationMazur, M. T., Cardasis, H. L., Spellman, D. S., Liaw, A., Yates, N. A., & Hendrickson, R. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910776107 · Cited by 87 · see citing works
A comprehensive pipeline for translational top-down proteomics from a single blood draw
Toby, T. K., Fornelli, L., Srzentić, K., DeHart, C. J., Levitsky, J., Friedewald, J., & Kelleher, N. L. (2019) · Nature Protocols · doi:10.1038/s41596-018-0085-7 · Cited by 86 · see citing works
Self-citationMelani, R. D., Skinner, O. S., Fornelli, L., Domont, G. B., Compton, P. D., & Kelleher, N. L. (2016) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m115.056523 · Cited by 85 · see citing works
Self-citationHan, X., Wang, Y., Aslanian, A., Bern, M., Lavallée-Adam, M., & Yates, J. R. (2014) · Analytical Chemistry · doi:10.1021/ac503439n · Cited by 77 · see citing works
pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification
Sun, R.-X., Luo, L., Wu, L., Wang, R.-M., Zeng, W.-F., Chi, H., Liu, C., & He, S.-M. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b03963 · Cited by 71 · see citing works
Zhou, M., Uwugiaren, N., Williams, S. M., Moore, R. J., Zhao, R., Goodlett, D., Dapic, I., Paša-Tolić, L., & Zhu, Y. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c00467 · Cited by 62 · see citing works
Fert-Bober, J., Murray, C. I., Parker, S. J., & Van Eyk, J. E. (2018) · Circulation Research · doi:10.1161/circresaha.118.310966 · Cited by 45 · see citing works
Accurate Estimation of Context-Dependent False Discovery Rates in Top-Down Proteomics
LeDuc, R. D., Fellers, R. T., Early, B. P., Greer, J. B., Shams, D. P., Thomas, P. M., & Kelleher, N. L. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra118.000993 · Cited by 44 · see citing works
Self-citationAnderson, L. C., English, A. M., Wang, W.-H., Bai, D. L., Shabanowitz, J., & Hunt, D. F. (2015) · International Journal of Mass Spectrometry · doi:10.1016/j.ijms.2014.06.023 · Cited by 37 · see citing works
Zhou, M., Paša-Tolić, L., & Stenoien, D. L. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00694 · Cited by 39 · see citing works
The benefits (and misfortunes) of SDS in top-down proteomics
Kachuk, C., & Doucette, A. A. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2017.03.002 · Cited by 39 · see citing works
Intact-Mass Analysis Facilitating the Identification of Large Human Heart Proteoforms
Schaffer, L. V., Tucholski, T., Shortreed, M. R., Ge, Y., & Smith, L. M. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02343 · Cited by 17 · see citing works
- Authors
- Zamdborg, L., LeDuc, R. D., Glowacz, K. J., Kim, Y.-B., Viswanathan, V., Spaulding, I. T., Early, B. P., Bluhm, E. J., Babai, S., & Kelleher, N. L.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Corresponding author
- LeDuc, R. D.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2007-05-08
- Volume
- 35
- Issue
- Web Server
- Pages
- W701-W706
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1933126
- OpenAlex
- W2131381861
- Cited by
- 251
- References
- 20
- Citations by year
- 2026: 6 · 2025: 7 · 2024: 8 · 2023: 12 · 2022: 5 · 2021: 14 · 2020: 10 · 2019: 13 · 2018: 15 · 2017: 20 · 2016: 14 · 2015: 18 · 2014: 25 · 2013: 17 · 2012: 16
- FWCI
- 5.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute on Drug Abuse (P30 DA 018310-039002, DA018310, P30DA018310)
- National Institute of General Medical Sciences (R01GM067193, GM 067193)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- top-down mass spectrometry, protein identification, protein characterization, terminal modification, multiplexing, data import and export
- MeSH terms
- Electronic Data Processing, Humans, Polymorphism, Genetic, Programming Languages, Protein Processing, Post-Translational, Proteins, Software, Mass Spectrometry, User-Computer Interface, Sequence Tagged Sites, Computational Biology, Internet, Sequence Analysis, Protein, Databases, Protein
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