@article{smith-2013,
	author = {Smith, Lloyd M and Kelleher, Neil L},
	journal = {Nature Methods},
	month = {2},
	number = {3},
	pages = {186--187},
	title = {{Proteoform: a single term describing protein complexity}},
	volume = {10},
	year = {2013},
	doi = {10.1038/nmeth.2369},
	url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC4114032/},
}
@article{angel-2012,
	author = {Angel, Thomas E. and Aryal, Uma K. and Hengel, Shawna M. and Baker, Erin S. and Kelly, Ryan T. and Robinson, Errol W. and Smith, Richard D.},
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	month = {1},
	number = {10},
	pages = {3912},
	title = {{Mass spectrometry-based proteomics: existing capabilities and future directions}},
	volume = {41},
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	url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC3375054/},
}
@article{leduc-2018,
	author = {LeDuc, Richard D. and Schwämmle, Veit and Shortreed, Michael R. and Cesnik, Anthony J. and Solntsev, Stefan K. and Shaw, Jared B. and Martin, Maria J. and Vizcaino, Juan A. and Alpi, Emanuele and Danis, Paul and Kelleher, Neil L. and Smith, Lloyd M. and Ge, Ying and Agar, Jeffrey N. and Chamot-Rooke, Julia and Loo, Joseph A. and Pasa-Tolic, Ljiljana and Tsybin, Yury O.},
	journal = {Journal of Proteome Research},
	month = {2},
	number = {3},
	pages = {1321--1325},
	title = {{ProForma: a standard proteoform notation}},
	volume = {17},
	year = {2018},
	doi = {10.1021/acs.jproteome.7b00851},
	url = {https://pmc.ncbi.nlm.nih.gov/articles/PMC5837035/},
}
@article{team-2025,
	author = {Team, Pandas Development},
	journal = {Zenodo (CERN European Organization for Nuclear Research)},
	month = {12},
	title = {{pandas-dev/pandas: Pandas}},
	year = {2025},
	doi = {10.5281/zenodo.17992932},
	url = {https://doi.org/10.5281/zenodo.17992932},
}
@article{vink-2025,
	author = {Vink, Ritchie and De Gooijer, Stijn and Beedie, Alexander and Burghoorn, Gijs and Nameexhaustion and Peters, Orson and Gorelli, Marco Edward and Reswqa and Van Zundert, Jeroen and Marshall and Hulselmans, Gert and Grinstead, Cory and Denecker, Koen and Manley, Luke and chielP and Turner-Trauring, Itamar and Valtar, Kuba and Mitchell, Lawrence and Sprenkels, Amber and Genockey, Karl and Eitsupi and Harbeck, Henry and Robin and Patyk, Kevin and Santamaria, Matteo and Borchert, Oliver and Deanm and Heres, Daniël and Magarick, Josh},
	journal = {Zenodo (CERN European Organization for Nuclear Research)},
	month = {12},
	title = {{pola-rs/polars: Python Polars 1.36.1}},
	year = {2025},
	doi = {10.5281/zenodo.17873635},
	url = {https://doi.org/10.5281/zenodo.17873635},
}
@article{goloborodko-2013,
	author = {Goloborodko, Anton A. and Levitsky, Lev I. and Ivanov, Mark V. and Gorshkov, Mikhail V.},
	journal = {Journal of the American Society for Mass Spectrometry},
	month = {1},
	number = {2},
	pages = {301--304},
	title = {{Pyteomics—A Python framework for exploratory data analysis and rapid software prototyping in proteomics}},
	volume = {24},
	year = {2013},
	doi = {10.1007/s13361-012-0516-6},
	url = {https://doi.org/10.1007/s13361-012-0516-6},
}
@article{cock-2009,
	author = {Cock, Peter J. A. and Antao, Tiago and Chang, Jeffrey T. and Chapman, Brad A. and Cox, Cymon J. and Dalke, Andrew and Friedberg, Iddo and Hamelryck, Thomas and Kauff, Frank and Wilczynski, Bartek and De Hoon, Michiel J. L.},
	journal = {Bioinformatics},
	month = {3},
	number = {11},
	pages = {1422--1423},
	title = {{Biopython: freely available Python tools for computational molecular biology and bioinformatics}},
	volume = {25},
	year = {2009},
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	url = {https://doi.org/10.1093/bioinformatics/btp163},
}
@software{Schulte_mzcore,
	author = {Schulte, Douwe and Gabriels, Ralf and Heerdink, Auke},
	license = {MIT OR Apache-2.0},
	title = {{mzcore}},
	url = {https://github.com/rusteomics/mzcore},
	version = {0.11.0}
}
@article{rost-2013,
	author = {Röst, Hannes L. and Schmitt, Uwe and Aebersold, Ruedi and Malmström, Lars},
	journal = {PROTEOMICS},
	month = {11},
	number = {1},
	pages = {74--77},
	title = {{pyOpenMS: A Python‐based interface to the OpenMS mass‐spectrometry algorithm library}},
	volume = {14},
	year = {2013},
	doi = {10.1002/pmic.201300246},
	url = {https://doi.org/10.1002/pmic.201300246},
}
@article{creasy-2004,
	author = {Creasy, David M. and Cottrell, John S.},
	journal = {PROTEOMICS},
	month = {4},
	number = {6},
	pages = {1534--1536},
	title = {{Unimod: Protein modifications for mass spectrometry}},
	volume = {4},
	year = {2004},
	doi = {10.1002/pmic.200300744},
	url = {https://doi.org/10.1002/pmic.200300744},
}

@misc{hupo-psi-no-date,
	author = {Hupo-Psi},
	title = {{GitHub - HUPO-PSI/psi-ms-CV: HUPO-PSI mass spectrometry CV}},
	url = {https://github.com/HUPO-PSI/psi-ms-CV},
}
@misc{hupo-psi-no-dateB,
	author = {Hupo-Psi},
	title = {{GitHub - HUPO-PSI/xlmod-CV: Repo for the XLMOD ontology for chemical cross linkers}},
	url = {https://github.com/HUPO-PSI/xlmod-CV},
}
@misc{unknown-author-no-date,
	title = {{RESID Database [PIR - Protein Information Resource]}},
	url = {https://proteininformationresource.org/resid/},
}
@misc{glygen-glycan-data-no-date,
	author = {Glygen-Glycan-Data},
	title = {{GitHub - glygen-glycan-data/GNOme: GNOme - Glycan Naming and Subsumption Ontology.}},
	url = {https://github.com/glygen-glycan-data/GNOme},
}
@software{garrett-2026-tacular,
	author = {Garrett, Patrick},
	title = {{tacular-omics/tacular: v1.0.1 - Zenodo + Docs}},
	version = {v1.0.1},
	year = {2026},
	publisher = {Zenodo},
	doi = {10.5281/zenodo.18475557},
	url = {https://doi.org/10.5281/zenodo.18475557},
}
@book{garrett-2025,
	author = {Garrett, Patrick T. and Turner, Natalie P. and Nakorchevsky, Alex and Pankow, Sandra and Yates, John R.},
	booktitle = {Elsevier eBooks},
	month = {1},
	title = {{Mass spectrometry-based proteomics}},
	year = {2025},
	doi = {10.1016/b978-0-323-99507-8.00013-5},
	url = {https://doi.org/10.1016/b978-0-323-99507-8.00013-5},
}