Reference

All functions
brunner2022	Brunner et al. 2022 (Mol. Syst. Biol.): cell cycle state study
cong2020AC	Cong et al. 2020 (Ana. Chem.): HeLa single cells
derks2022	Derks et al. 2022 - plexDIA (Nat. Biotechnol.): PDAC vs melanoma cells vs monocytes
dou2019_boosting	Dou et al. 2019 (Anal. Chem.): testing boosting ratios
dou2019_lysates	Dou et al. 2019 (Anal. Chem.): HeLa lysates
dou2019_mouse	Dou et al. 2019 (Anal. Chem.): murine cell lines
gregoire2023_mixCTRL	Grégoire et al. 2023 - mixCTRL (arXiv): benchmark using monocytes/macrophages
guise2024	Guise et al. 2020 (Cell Rep.): postmortem ALS spinal moto neurons
khan2023	Khan et al, 2023 (biorRxiv): Epithelial–Mesenchymal Transition
leduc2022()	Deprecated leduc2022 dataset
leduc2022_pSCoPE	Leduc et al. 2022 - pSCoPE (biorRxiv): melanoma cells vs monocytes
leduc2022_plexDIA	Leduc et al. 2022 - plexDIA (biorRxiv): melanoma cells
liang2020_hela	Liang et al. 2020 (Anal. Chem.): HeLa cells (MaxQuant preprocessing)
petrosius2023_AstralAML	Petrosius et al. 2023 (bioRxiv): AML hierarchy on Astral.
petrosius2023_mES	Petrosius et al, 2023 (Nat. Comm.): Mouse embryonic stem cell (mESC) in different culture conditions
schoof2021	Schoof et al. 2021 (Nat. Comm.): acute myeloid leukemia differentiation
scpdata()	Single-Cell Proteomics Data Package
specht2019v2	Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 2)
specht2019v3	Specht et al. 2019 - SCoPE2 (biorRxiv): macrophages vs monocytes (version 3)
williams2020_lfq	Williams et al. 2020 (Anal. Chem.): MCF10A cell line
williams2020_tmt	Williams et al. 2020 (Anal. Chem.): 3 AML cell line
woo2022_lung	Woo et al. 2022 (Cell Syst.): 26 primary human lung cells
woo2022_macrophage	Woo et al. 2022 (Cell Syst.): LPS-treated macrophages
zhu2018MCP	Zhu et al. 2018 (Mol. Cel. Prot.): rat brain laser dissections
zhu2018NC_hela	Zhu et al. 2018 (Nat. Comm.): HeLa titration
zhu2018NC_islets	Zhu et al. 2018 (Nat. Comm.): human pancreatic islets
zhu2018NC_lysates	Zhu et al. 2018 (Nat. Comm.): HeLa lysates
zhu2019EL	Zhu et al. 2019 (eLife): chicken utricle cells