My Publications
A collection of scholarly research and other peer-reviewed work I have written or contributed to. I was a graduate student at Boston University from 2014 to 2019, working under the supervision of Joseph Zaia and Luis Carvalho.
From 2019 to 2025, I was employed by Gritstone bio, but continued to develop my dissertation work throughout that period on my own time.
2024
- Klein, Joshua, Carvalho, Luis, Zaia, Joseph. Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity, Nature CommunicationsPublished at http://dx.doi.org/10.1038/s41467-024-50338-5
- Klein, Joshua, Lam, Henry, Mak, Tytus D., Bittremieux, Wout, Perez-Riverol, Yasset, Gabriels, Ralf, Shofstahl, Jim, Hecht, Helge, Binz, Pierre-Alain, Kawano, Shin, Van Den Bossche, Tim, Carver, Jeremy, Neely, Benjamin A., Mendoza, Luis, Suomi, Tomi, Claeys, Tine, Payne, Thomas, Schulte, Douwe, Sun, Zhi, Hoffmann, Nils, Zhu, Yunping, Neumann, Steffen, Jones, Andrew R., Bandeira, Nuno, Vizcaíno, Juan Antonio, Deutsch, Eric W.. The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF, Analytical ChemistryPublished at https://pubs.acs.org/doi/10.1021/acs.analchem.4c04091
2023
- Palmer, Christine D., Scallan, Ciaran D., Kraemer-Tardif, Lauren D., Kachura, Melissa A., Rappaport, Amy R., Koralek, Daniel O., Uriel, Alison, Gitlin, Leonid, Klein, Joshua, Davis, Matthew J., Venkatraman, Harshni, Hart, Meghan G., Jaroslavsky, Jason R., Kounlavouth, Sonia, Marrali, Martina, Nganje, Charmaine N., Bae, Kyounghwa, Yan, Tiffany, Leodones, Katharyn, Egorova, Milana, Hong, Sue-Jean, Kuan, Jenchun, Grappi, Silvia, Garbes, Pedro, Jooss, Karin, Ustianowski, Andrew. GRT-R910: a self-amplifying mRNA SARS-CoV-2 vaccine boosts immunity for ≥6 months in previously-vaccinated older adults, Nature CommunicationsPublished at https://www.nature.com/articles/s41467-023-39053-9
2022
- Leduc, Richard D, Deutsch, Eric W, Fellers, Ryan T, Anthony, J, Klein, Joshua A, Bossche, Tim Van Den, Gabriels, Ralf, Pullman, Benjamin, Bandeira, Nuno, Kelleher, Neil L, Paul, M. Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms, Journal of Proteome ResearchPublished at https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00771
2021
- Chang, Deborah, Klein, Joshua A., Nalehua, Mary Rachel, Hackett, William E., Zaia, Joseph. Data-independent acquisition mass spectrometry for site-specific glycoproteomics characterization of SARS-CoV-2 spike protein, Analytical and Bioanalytical Chemistry
- Deutsch, Eric W., Perez-Riverol, Yasset, Carver, Jeremy, Kawano, Shin, Mendoza, Luis, Van Den Bossche, Tim, Gabriels, Ralf, Binz, Pierre Alain, Pullman, Benjamin, Sun, Zhi, Shofstahl, Jim, Bittremieux, Wout, Mak, Tytus D., Klein, Joshua, Zhu, Yunping, Lam, Henry, Vizcaíno, Juan Antonio, Bandeira, Nuno. Universal Spectrum Identifier for mass spectra, Nature MethodsPublished at http://dx.doi.org/10.1038/s41592-021-01184-6
- Hogan, John D., Wu, Jiandong, Klein, Joshua A., Lin, Cheng, Carvalho, Luis, Zaia, Joseph. GAGrank: Software for glycosaminoglycan sequence ranking using a bipartite graph model, Molecular and Cellular ProteomicsPublished at https://doi.org/10.1016/j.mcpro.2021.100093
2020
- Klein, Joshua, Zaia, Joseph. Relative Retention Time Estimation Improves N-Glycopeptide Identifications by LC–MS/MS, Journal of Proteome ResearchPublished at https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00051
2019
- Klein, Joshua, Zaia, Joseph. psims - A Declarative Writer for mzML and mzIdentML for Python, Molecular & Cellular ProteomicsPublished at http://www.mcponline.org/lookup/doi/10.1074/mcp.RP118.001070
- Klein, Joshua, Zaia, Joseph. glypy: An Open Source Glycoinformatics Library, Journal of Proteome ResearchPublished at http://pubs.acs.org/doi/10.1021/acs.jproteome.9b00367
- Levitsky, Lev I., Klein, Joshua A., Ivanov, Mark V., Gorshkov, Mikhail V.. Pyteomics 4.0: Five Years of Development of a Python Proteomics Framework, Journal of Proteome ResearchPublished at http://pubs.acs.org/doi/10.1021/acs.jproteome.8b00717
- Raghunathan, Rekha, Sethi, Manveen K., Klein, Joshua A., Zaia, Joseph. Proteomics, glycomics, and glycoproteomics of matrisome molecules, Molecular and Cellular ProteomicsPublished at http://dx.doi.org/10.1074/mcp.R119.001543
- Raghunathan, Rekha, Sethi, Manveen K., Klein, Joshua A., Zaia, Joseph. Proteomics, Glycomics, and Glycoproteomics of Matrisome Molecules, Molecular & Cellular ProteomicsPublished at http://www.mcponline.org/lookup/doi/10.1074/mcp.R119.001543
2018
- Klein, Joshua, Carvalho, Luis, Zaia, Joseph. Application of network smoothing to glycan LC-MS profiling, BioinformaticsPublished at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty397/5001382
- Klein, Joshua A, Meng, Le, Zaia, Joseph. Deep Sequencing of Complex Proteoglycans: A Novel Strategy for High Coverage and Site-specific Identification of Glycosaminoglycan-linked Peptides, Molecular & Cellular ProteomicsPublished at http://www.mcponline.org/content/early/2018/05/17/mcp.RA118.000766.full.pdf
- Hogan, John D, Klein, Joshua A, Wu, Jiandong, Chopra, Pradeep, Boons, Geert-Jan, Carvalho, Luis, Lin, Cheng, Zaia, Joseph. Software for peak finding and elemental composition assignment for glycosaminoglycan tandem mass spectra, Molecular & Cellular ProteomicsPublished at http://www.ncbi.nlm.nih.gov/pubmed/29615495
- Khatri, Kshitij, Pu, Yi, Klein, Joshua A., Wei, Juan, Costello, Catherine E., Lin, Cheng, Zaia, Joseph. Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides, Journal of The American Society for Mass SpectrometryPublished at http://www.ncbi.nlm.nih.gov/pubmed/29663256
- Kösters, M, Leufken, J, Schulze, S, Sugimoto, K, Klein, J, Zahedi, R P, Hippler, M, Leidel, S A, Fufezan, C. pymzML v2.0: introducing a highly compressed and seekable gzip format, BioinformaticsPublished at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty046/4831092
- Raghunathan, Rekha, Polinski, Nicole K., Klein, Joshua A., Hogan, John D., Shao, Chun, Khatri, Kshitij, Leon, Deborah R., McComb, Mark E., Manfredsson, Fredric P., Sortwell, Caryl E., Zaia, Joseph. Glycomic and Proteomic changes in aging brain nigrostriatal pathway, Molecular & Cellular ProteomicsPublished at http://www.mcponline.org/lookup/doi/10.1074/mcp.RA118.000680
- Wu, Jiandong, Wei, Juan, Hogan, John D., Chopra, Pradeep, Joshi, Apoorva, Lu, Weigang, Klein, Joshua, Boons, Geert-Jan, Lin, Cheng, Zaia, Joseph. Negative Electron Transfer Dissociation Sequencing of 3-O-Sulfation-Containing Heparan Sulfate Oligosaccharides, Journal of The American Society for Mass SpectrometryPublished at http://link.springer.com/10.1007/s13361-018-1907-0
2017
- Haserick, J.R., Klein, J.A., Costello, C.E., Samuelson, J.. Cryptosporidium parvum vaccine candidates are incompletely modified with O-linked-N-acetylgalactosamine or contain N-terminal N-myristate and S-palmitate, PLoS ONE
- Khatri, Kshitij, Klein, Joshua A., Haserick, John R., Leon, Deborah R., Costello, Catherine E., McComb, Mark E., Zaia, Joseph. Microfluidic Capillary Electrophoresis–Mass Spectrometry for Analysis of Monosaccharides, Oligosaccharides, and Glycopeptides, Analytical ChemistryPublished at http://pubs.acs.org/doi/abs/10.1021/acs.analchem.7b00875
2016
- Hu, Han, Khatri, Kshitij, Klein, Joshua, Leymarie, Nancy, Zaia, Joseph. A review of methods for interpretation of glycopeptide tandem mass spectral data, Glycoconjugate JournalPublished at http://link.springer.com/10.1007/s10719-015-9633-3
- Khatri, Kshitij, Klein, Joshua A, White, Mitchell R., Grant, Oliver C., Leymarie, Nancy, Woods, Robert J., Hartshorn, Kevan L., Zaia, Joseph. Integrated Omics and Computational Glycobiology Reveal Structural Basis for Influenza A Virus Glycan Microheterogeneity and Host Interactions, Molecular & Cellular ProteomicsPublished at http://www.ncbi.nlm.nih.gov/pubmed/26984886
- Khatri, Kshitij, Klein, Joshua A., Zaia, Joseph. Use of an informed search space maximizes confidence of site-specific assignment of glycoprotein glycosylation, Analytical and Bioanalytical ChemistryPublished at http://link.springer.com/10.1007/s00216-016-9970-5
- Zaia, Joseph, Khatri, Kshitij, Klein, Joshua, Shao, Chun, Sheng, Yuewei, Viner, Rosa. Complete Molecular Weight Profiling of Low-Molecular Weight Heparins Using Size Exclusion Chromatography-Ion Suppressor-High-Resolution Mass Spectrometry, Analytical ChemistryPublished at http://pubs.acs.org/doi/abs/10.1021/acs.analchem.6b03081
2013
- Garrett, Teresa A., Schmeitzel, John L., Klein, Joshua A., Hwang, Janice J., Schwarz, Jodi A.. Comparative lipid profiling of the cnidarian Aiptasia pallida and its dinoflagellate symbiont., PloS onePublished at http://www.ncbi.nlm.nih.gov/pubmed/23483956