MASH Explorer: A Universal Software Environment for Top-Down Proteomics
Open accessAbstract
Top-down mass spectrometry (MS)-based proteomics enable a comprehensive analysis of proteoforms with molecular specificity to achieve a proteome-wide understanding of protein functions. However, the lack of a universal software for top-down proteomics is becoming increasingly recognized as a major barrier, especially for newcomers. Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics. MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time. It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide. With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will play an integral role in advancing top-down proteomics to realize its full potential for biomedical research.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
0 of 18 cited sources checked · 0 supported · 0 flagged
- Findingown data
With MASH Explorer, z•15, z•16, z•23, and z•24 ions were visualized to locate Cys220 as the payload site for an Fd1 subunit isomer.
“z•15, z•16, z•23, and z•24 ions were visualized using the Ion Finder Tool to localize Cys220 as the site for the payload for an Fd1 subunit isomer (Figure 5B).”
Quote in the paperSubstantial claim - Findingnone given
MASH Explorer is available without charge to users globally.
“It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide.”
- Also stated in: § INTRODUCTION · plain
“Here, we have developed MASH Explorer, a universal, comprehensive, user-friendly, and freely available software environment for top-down proteomics (http://ge.crb.wisc.edu/MASH_Explorer/index.htm).”
- Also stated in: § DISCUSSION · plain
“MASH Explorer is a nonproprietary and free software solution, providing a universal and comprehensive environment for processing top-down proteomics data.”
Quote in the paperSubstantial claim - Also stated in: § INTRODUCTION · plain
- Findingreasoning
MASH Explorer combines several spectral deconvolution and database search algorithms within one platform.
“MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time.”
- Also stated in: § RESULTS · plain
“For the first time, MASH Explorer integrates multiple deconvolution and database search algorithms into a single platform to maximize the performance for enhanced protein identification (Figure 1).”
Quote in the paperSubstantial claim - Also stated in: § RESULTS · plain
- Findingcitation
MASH Explorer incorporates multiple deconvolution algorithms, including MS-Deconv, TopFD, eTHRASH, pParseTD, and ProMex.
“Currently, the software incorporates various deconvolution algorithms including MS-Deconv,17 TopFD,14 eTHRASH,19 pParseTD,15 and ProMex26 for both MS and MS/MS deconvolution.”
Quote in the paperSubstantial claim0 of 3 sources checked - Findingcitation
MASH Explorer can be used to characterize the subunits of antibody-drug conjugates.
“Moreover, MASH Explorer can also be extended to characterize the subunits of ADCs,24 which combine the target specificity of monoclonal antibody and the potency of the cytotoxin drugs, gaining enormous interest in the pharmaceutical industry (Figure 5 and Figure 6).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [24] source
Not checked in the free run.
- Findingreasoning
MASH Explorer is able to handle top-down proteomics data produced in different vendor formats.
“MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time.”
- Also stated in: § INTRODUCTION · plain
“This software can process high-resolution MS, MS/MS, and liquid-chromatography tandem MS (LC-MS/MS) data across multiple vendor-specific formats, with automated database searching for protein identification as well as user-friendly tools for proteoform characterization and data visualization/validation.”
- Also stated in: § RESULTS · plain
“One unique feature of MASH Explorer is its universal data processing platform for top-down proteomics with the capability to process data from multiple vendor formats.”
Quote in the paperSubstantial claim - Also stated in: § INTRODUCTION · plain
- Findingreasoning
MASH Explorer contains a Targeted Mode workflow for detailed proteoform characterization, including PTMs and sequence variants.
“MASH Explorer includes two major workflows: “Discovery Mode” for analysis of complex high-resolution LC-MS/MS data to achieve global protein identification and “Targeted Mode” for comprehensive proteoform characterization including PTMs and sequence variants, with user-friendly graphic user interface (GUI) support.”
- Also stated in: § RESULTS · plain
“Another important feature of MASH Explorer is a complementary “Targeted Mode” workflow that is optimized for the detailed and comprehensive characterization of individual proteins, enabling users to identify site-specific PTMs within a protein target (Figure 4).”
Quote in the paperSubstantial claim - Also stated in: § RESULTS · plain
- Findingcitation
MASH Explorer imports data using ProteoWizard, DeconEngine, and vendor-provided libraries.
“Importing data obtained from different MS instruments is supported using ProteoWizard,12 DeconEngine,13 and vendor provided libraries.”
- Also stated in: § RESULTS · plain
“The data import function is supported by ProteoWizard,12 DeconEngine,13 and vendor provided libraries.”
Quote in the paperSubstantial claim0 of 2 sources checked - Also stated in: § RESULTS · plain
- Findingreasoning
MASH Explorer offers a graphical interface for visualizing LC chromatograms, mass spectra, and fragment ion maps.
“MASH Explorer provides GUI to visualize experimental data for LC chromatograms, mass spectra, and fragment ion maps generated from various MS/MS experiments such as CID, ECD/ETD, and UVPD.”
Quote in the paperNot a substantial claim - Findingown data
Combining various deconvolution and database search algorithms in MASH Explorer improves global proteoform identification and characterization.
“Incorporation of various deconvolution and database search algorithms enables MASH Explorer to improve global proteoform identification and characterization (Figure 3 and Figure S5).”
Quote in the paperSubstantial claim - Findingown data
MASH Explorer incorporates multiple database search algorithms, including MS-Align+, TopPIC, pTop, and MSPathFinderT.
“The database search algorithms such as MS-Align+,18 TopPIC,14 pTop,15 and MSPathFinderT26 were integrated in the software for protein identification.”
Quote in the paperSubstantial claim0 of 3 sources checked - Findingreasoning
MASH Explorer can incorporate additional algorithms because of its modular design.
“In addition to the current list of deconvolution and database search algorithms, MASH Explorer has the capability to incorporate more algorithms, owing to the modularity of the software.”
Quote in the paperNot a substantial claim - Findingreasoning
MASH Explorer contains a Discovery Mode workflow for analyzing complex LC-MS/MS data to identify proteins on a global scale.
“MASH Explorer includes two major workflows: “Discovery Mode” for analysis of complex high-resolution LC-MS/MS data to achieve global protein identification and “Targeted Mode” for comprehensive proteoform characterization including PTMs and sequence variants, with user-friendly graphic user interface (GUI) support.”
- Also stated in: § RESULTS · plain
“MASH Explorer features a “Discovery Mode” workflow that is useful for high-throughput data processing and proteoform identification from batch LC-MS/MS raw data files without a priori knowledge of specific proteins (Figure 2).”
Quote in the paperSubstantial claim - Also stated in: § RESULTS · plain
- Interpretationreasoning
MASH Explorer is the first platform to combine multiple deconvolution and database search algorithms into one system capable of processing top-down proteomics data from different vendor formats.
“MASH Explorer integrates multiple spectral deconvolution and database search algorithms into a single, universal platform which can process top-down proteomics data from various vendor formats, for the first time.”
- Also stated in: § RESULTS · plain
“For the first time, MASH Explorer integrates multiple deconvolution and database search algorithms into a single platform to maximize the performance for enhanced protein identification (Figure 1).”
Quote in the paperSubstantial claim - Also stated in: § RESULTS · plain
- Premisecitation
A major obstacle, particularly for newcomers, is the shortage of a general, easy-to-use program for streamlined analysis of complex top-down proteomics data, which restricts the field's broader impact.
“Particularly, the lack of a universal and user-friendly software for streamlined analysis of complex top-down proteomics data is becoming increasingly recognized as a major barrier, especially for newcomers, thus limiting the broader impact of top-down proteomics in the biomedical research communities.”
Quote in the paperSubstantial claim0 of 3 sources checked - Interpretationreasoning
MASH Explorer functions as a general-purpose software platform for top-down proteomics.
“Here, we have developed MASH Explorer, a universal, comprehensive, and user-friendly software environment for top-down proteomics.”
- Also stated in: § INTRODUCTION · plain
“Here, we have developed MASH Explorer, a universal, comprehensive, user-friendly, and freely available software environment for top-down proteomics (http://ge.crb.wisc.edu/MASH_Explorer/index.htm).”
- Also stated in: § DISCUSSION · plain
“MASH Explorer is a nonproprietary and free software solution, providing a universal and comprehensive environment for processing top-down proteomics data.”
Quote in the paperSubstantial claim - Also stated in: § INTRODUCTION · plain
- Interpretationreasoning
MASH Explorer offers a general and comprehensive setting for processing top-down proteomics data.
“MASH Explorer is a nonproprietary and free software solution, providing a universal and comprehensive environment for processing top-down proteomics data.”
Quote in the paperSubstantial claim
- May combine two claims. 6
- Classified as probably not a substantial claim. 5
May combine two claims.
Findingown dataMASH Explorer accepts raw data formats from Thermo, Bruker, and Waters, as well as universal formats mzXML and mgf.
“MASH Explorer currently support specific vendor raw data formats from Thermo (.raw), Bruker (.d and .ascii), and Waters (.raw) (Figure 1). Moreover, universal data formats such as mzXML and mgf can be imported.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingnone givenMASH Explorer is nonproprietary.
“MASH Explorer is a nonproprietary and free software solution, providing a universal and comprehensive environment for processing top-down proteomics data.”
Quote in the paperNot a substantial claimMay combine two claims.
FindingreasoningMASH Explorer's Ion Finder Tool processes ion lists from different fragmentation methods to annotate proteoforms and match theoretical with observed fragment ions.
“In addition to the functions introduced in our previous generation software, MASH Suite Pro,11 which provides tools for users to perform charge state and mass shift correction, the “Targeted Mode” in MASH Explorer introduces an Ion Finder Tool GUI that parses through generated ion lists from different fragmentation methods to find proteoform annotations and allow users to match theoretical and obs”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataMASH software has drawn users from North America, Europe, and Asia.
“While the majority of users are from North America, the MASH software has continuously attracted users across the globe, including users from continents such as Europe and Asia.”
Quote in the paperNot a substantial claimMay combine two claims.
FindingreasoningMASH Explorer provides a Process Wizard and a Workflow Manager to support high-throughput data processing.
“MASH Explorer has many new features including (1) development of a universal platform for streamlined data processing from various vendor formats to standardize the data analysis; (2) integration of multiple deconvolution and database search algorithms for significantly enhanced protein identification; (3) workflow management for high-throughput data processing using the Process Wizard and Workfl”
- Also stated in: § RESULTS · plain
“MASH Explorer implements the Process Wizard, a user-friendly GUI to allow users to easily select deconvolution and database search algorithms and to customize the parameters of the selected algorithms for data processing, which is particularly convenient for users.”
- Also stated in: § RESULTS · plain
“Additionally, MASH Explorer implements a Workflow Manager to enhance the efficiency of processing top-down proteomics data sets (Figure S4).”
Quote in the paperSubstantial claim- Also stated in: § RESULTS · plain
Probably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataAs of March 24, 2020, MASH Explorer had been downloaded and used by over 600 users worldwide.
“Since the development of the MASH project, the software has been downloaded and used by more than 600 users around the world (as of March 24th, 2020) (Figure 7).”
Quote in the paperNot a substantial claimMay combine two claims.
PremisecitationA machine learning tool used hierarchical clustering to merge deconvoluted peak lists from different algorithms, which effectively detects true positive peaks while filtering false positives, leading to improved accuracy and confidence in protein identification.
“This machine learning tool used hierarchical clustering to combine deconvoluted peak lists from different algorithms, which can effectively detect true positive peaks while filtering out false positive peaks, resulting in enhanced accuracy and confidence in protein identification during database search.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [23] source
Not checked in the free run.
May combine two claims.
Interpretationnone givenMASH Explorer's main innovations include combining multiple deconvolution and search algorithms into one general platform that processes raw data from different vendor formats through a user-friendly interface.
“The major innovations of MASH Explorer include the integration of multiple deconvolution and search algorithms into a single, universal platform to process raw data from various vendor formats in a user-friendly interface.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisereasoningMASH Suite and MASH Suite Pro are earlier generations of proteomics software.
“Advancing on our previous generations of proteomics software, MASH Suite10 and MASH Suite Pro,11 MASH Explorer has many new features including (1) development of a universal platform for streamlined data processing from various vendor formats to standardize the data analysis; (2) integration of multiple deconvolution and database search algorithms for significantly enhanced protein identification;”
Quote in the paperNot a substantial claim0 of 2 sources checkedMay combine two claims.
PremisecitationSoftware for analyzing protein-based top-down proteomics is still immature, largely because high-resolution intact protein mass spectra are extremely complex to handle.
“In contrast to the well-developed software packages in the peptide-based bottom-up proteomics, the data analysis tools for protein-based top-down proteomics remain under-developed due to the major challenge in handling the enormous complexity of high-resolution intact protein mass spectra.7–9”
Quote in the paperSubstantial claim0 of 3 sources checkedProbably not a substantial claim: may not pass S2 (checkable), S4 (based).
InterpretationreasoningMASH Explorer meets an urgent need within the rapidly expanding top-down proteomics community.
“It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide.”
Quote in the paperNot a substantial claim- Rests on an assumption: The top-down proteomics community has an urgent need for a universal, comprehensive, and globally accessible software.
- Rests on an assumption: The top-down proteomics community is rapidly growing.
The paper relies on this without support.
The top-down proteomics community has an urgent need for a universal, comprehensive, and globally accessible software.
“It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide.”
“With the critical need and tremendous support from the community, we envision that this MASH Explorer software package will serve as a powerful tool to enable top-down proteomics researchers worldwide, playing an integral role in advancing top-down proteomics to realize its full potential for biomedical research.”
The paper relies on this without support.
Commercial top-down software is relatively high cost, limiting accessibility for general users.
“Additionally, the relatively high cost of commercial top-down software limits the accessibility for general users and thus necessitates a freely available academic version.”
The paper relies on this without support.
The top-down proteomics community is rapidly growing.
“It addresses the urgent need in the rapidly growing top-down proteomics community and is freely available to all users worldwide.”
“As the burgeoning top-down proteomics community continues its rapid growth and has gained momentum through the creation of the Consortium for Top-Down Proteomics (CTDP) (http://www.topdownproteomics.org/), the need for universal, comprehensive, and globally accessible top-down proteomics software has increased tremendously.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
MASH Explorer integrates multiple spectral deconvolution and database searching algorithms into a single freely available universal platform that can process top-down proteomics data from various vendor formats.
“recently the Ge group developed MASH Explorer, which integrates multiple spectral deconvolution and database searching algorithms into a single, freely-available universal platform that can process top-down proteomics data from various vendor formats [139].”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [139]
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 [117]
Cites
ProteoWizard: open source software for rapid proteomics tools development
Kessner, D., Chambers, M., Burke, R., Agus, D., & Mallick, P. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn323 · Cited by 2,024 · see citing works
Marty, M. T., Baldwin, A. J., Marklund, E. G., Hochberg, G. K. A., Benesch, J. L. P., & Robinson, C. V. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b00140 · Cited by 1,000 · see citing works
How many human proteoforms are there?
Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2576 · Cited by 907 · see citing works
Self-citationAutomated 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
Decoding protein modifications using top-down mass spectrometry
Siuti, N., & Kelleher, N. L. (2007) · Nature Methods · doi:10.1038/nmeth1097 · Cited by 503 · see citing works
Proteoforms as the next proteomics currency
Smith, L. M., & Kelleher, N. L. (2018) · Science · doi:10.1126/science.aat1884 · Cited by 322 · see citing works
Kou, Q., Xun, L., & Liu, X. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw398 · Cited by 276 · see citing works
Self-citationJaitly, N., Mayampurath, A., Littlefield, K., Adkins, J. N., Anderson, G. A., & Smith, R. D. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-87 · Cited by 217 · see citing works
Top-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
Self-citationIdentification 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-citationTran, J. C., & Doucette, A. A. (2008) · Analytical Chemistry · doi:10.1021/ac702197w · Cited by 206 · 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
Self-citationProtein 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
Self-citationInformed-Proteomics: open-source software package for top-down proteomics
Park, J., Piehowski, P., Wilkins, C. S., Zhou, M., Mendoza, J., Fujimoto, G. M., Gibbons, B. C., Shaw, J., Shen, Y., Shukla, A. K., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4388 · Cited by 153 · 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
Self-citationA photocleavable surfactant for top-down proteomics
Brown, K. A., Chen, B., Guardado-Alvarez, T. M., Lin, Z., Hwang, L., Ayaz-Guner, S., Jin, S., & Ge, Y. (2019) · Nature Methods · doi:10.1038/s41592-019-0391-1 · Cited by 111 · see citing works
Self-citationTop-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
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
PP2A-B′ holoenzyme substrate recognition, regulation and role in cytokinesis
Wu, C.-G., Chen, H., Guo, F., Yadav, V. K., Mcilwain, S. J., Rowse, M., Choudhary, A., Lin, Z., Li, Y., Gu, T., et al. (2017) · Cell Discovery · doi:10.1038/celldisc.2017.27 · Cited by 85 · see citing works
Self-citationFLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics
Jeong, K., Kim, J., Gaikwad, M., Hidayah, S. N., Heikaus, L., Schlüter, H., & Kohlbacher, O. (2020) · Cell Systems · doi:10.1016/j.cels.2020.01.003 · Cited by 82 · see citing works
Guner, H., Close, P. L., Cai, W., Zhang, H., Peng, Y., Gregorich, Z. R., & Ge, Y. (2014) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-013-0789-4 · Cited by 73 · see citing works
Self-citationA five-level classification system for proteoform identifications
Smith, L., Thomas, P. M., Shortreed, M. R., Schaffer, L. V., Fellers, R. T., LeDuc, R. D., Tucholski, T., Ge, Y., Agar, J. N., Anderson, L. C., et al. (2019) · Nature Methods · doi:10.1038/s41592-019-0573-x · Cited by 72 · see citing works
Self-citationpTop 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
Self-citationSrzentić, K., Nagornov, K. O., Fornelli, L., Lobas, A. A., Ayoub, D., Kozhinov, A. N., Gasilova, N., Menin, L., Beck, A., Gorshkov, M. V., et al. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02398 · Cited by 55 · see citing works
Middle-Down Multi-Attribute Analysis of Antibody-Drug Conjugates with Electron Transfer Dissociation
Chen, B., Lin, Z., Zhu, Y., Jin, Y., Larson, E., Xu, Q., Fu, C., Zhang, Z., Zhang, Q., Pritts, W. A., et al. (2019) · Analytical Chemistry · doi:10.1021/acs.analchem.9b02194 · Cited by 38 · see citing works
Self-citationA Universal Score for Deconvolution of Intact Protein and Native Electrospray Mass Spectra
Marty, M. T. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.9b05272 · Cited by 35 · see citing works
Roberts, D. S., Chen, B., Tiambeng, T. N., Wu, Z., Ge, Y., & Jin, S. (2019) · Nano Research · doi:10.1007/s12274-019-2418-4 · Cited by 33 · see citing works
Self-citationMehaffey, M., Sanders, J. D., Holden, D., Nilsson, C., & Brodbelt, J. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b02099 · Cited by 33 · see citing works
Rana, A. S. J. B., Ge, Y., & Strieter, E. R. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00381 · Cited by 30 · see citing works
Self-citationJin, Y., Diffee, G., Colman, R., Anderson, R. M., & Ge, Y. (2019) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-019-02139-0 · Cited by 27 · see citing works
Self-citationMcIlwain, S. J., Wu, Z., Wetzel, M., Belongia, D., Jin, Y., Wenger, K., Ong, I. M., & Ge, Y. (2020) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.0c00035 · Cited by 27 · see citing works
Self-citationBack Cover: 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.201970085 · Cited by 9 · see citing works
Self-citationCrowe, S. O., Rana, A. S. J. B., Deol, K. K., et al. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02855 · Cited by 2 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- 10.1038/nmeth.4388 · DOI
Cited by
Sorted by citations
Top-down proteomics: challenges, innovations, and applications in basic and clinical research
Brown, K. A., Melby, J. A., Roberts, D. S., & Ge, Y. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1855982 · Cited by 152 · see citing works
Self-citationZhou, 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
Self-citationLarson, E. J., Zhu, Y., Wu, Z., Chen, B., Zhang, Z., Zhou, S., Han, L., Zhang, Q., & Ge, Y. (2020) · Analytical Chemistry · doi:10.1021/acs.analchem.0c03152 · Cited by 21 · see citing works
Self-citation
- Authors
- 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.
- Affiliations
- University of Wisconsin–Madison (US)
- Indiana University Indianapolis (US)
- National Institute of Biological Sciences, Beijing, 102206, China
- Corresponding author
- McIlwain, Sean J.
- Ge, Ying
- ORCID
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2020-08-04
- Volume
- 19
- Issue
- 9
- Pages
- 3867-3876
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC7728713
- OpenAlex
- W3046987053
- Cited by
- 76
- References
- 33
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 12 · 2023: 21 · 2022: 14 · 2021: 13 · 2020: 5
- FWCI
- 5.06
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Purdue University Indianapolis (Indiana University) (submittedVersion)
- Author eBooks
- Funders
- National Heart, Lung, and Blood Institute (R01 HL096971)
- Office of the Director (S10 OD018475)
- National Institute of General Medical Sciences (R01 GM117058, R01 GM125085)
- 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 proteomics, proteoforms, spectral deconvolution, database search algorithms, mass spectrometry data processing, software platform
- MeSH terms
- Algorithms, Software, Mass Spectrometry, Proteome, Proteomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-05.
Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-05.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
