Gatto, Laurent, Ruedi Aebersold, Juergen Cox, et al. 2023.
“Initial Recommendations for Performing, Benchmarking and
Reporting Single-Cell Proteomics Experiments.” Nat.
Methods 20 (3): 375–86.
Goeminne, Ludger J E, Kris Gevaert, and Lieven Clement. 2016.
“Peptide-Level Robust Ridge Regression Improves Estimation,
Sensitivity, and Specificity in Data-Dependent Quantitative Label-Free
Shotgun Proteomics.” Mol. Cell. Proteomics 15 (2):
657–68.
Huang, Ting, Meena Choi, Manuel Tzouros, et al. 2020.
“MSstatsTMT: Statistical Detection of Differentially
Abundant Proteins in Experiments with Isobaric Labeling and Multiple
Mixtures.” Mol. Cell. Proteomics 19 (10): 1706–23.
O’Brien, Jonathon J, Anil Raj, Aleksandr Gaun, et al. 2024. “A
Data Analysis Framework for Combining Multiple Batches Increases the
Power of Isobaric Proteomics Experiments.” Nat. Methods
21 (2): 290–300.
Plubell, Deanna L, Phillip A Wilmarth, Yuqi Zhao, et al. 2017.
“Extended Multiplexing of Tandem Mass Tags (TMT)
Labeling Reveals Age and High Fat Diet Specific Proteome Changes in
Mouse Epididymal Adipose Tissue.” Mol. Cell. Proteomics
16 (5): 873–90.
Ramond, Elodie, Gael Gesbert, Ida Chiara Guerrera, et al. 2015.
“Importance of Host Cell Arginine Uptake in Francisella Phagosomal
Escape and Ribosomal Protein Amounts.” Mol. Cell.
Proteomics 14 (4): 870–81.
Savitski, Mikhail M, Gavain Sweetman, Manor Askenazi, et al. 2011.
“Delayed Fragmentation and Optimized Isolation Width Settings for
Improvement of Protein Identification and Accuracy of Isobaric Mass Tag
Quantification on Orbitrap-Type Mass Spectrometers.” Anal.
Chem. 83 (23): 8959–67.
Segers, Alexandre, Cristian Castiglione, Christophe Vanderaa, et al.
2025. “omicsGMF: A Multi-Tool for
Dimensionality Reduction, Batch Correction and Imputation Applied to
Bulk- and Single Cell Proteomics Data.” bioRxiv, March,
2025.03.24.644996.
Shen, Xiaomeng, Shichen Shen, Jun Li, et al. 2018.
“IonStar Enables High-Precision, Low-Missing-Data
Proteomics Quantification in Large Biological Cohorts.” Proc.
Natl. Acad. Sci. U. S. A. 115 (21): E4767–76.
Staes, An, Teresa Mendes Maia, Sara Dufour, et al. 2024.
“Benefit
of in Silico Predicted Spectral Libraries in Data‑independent
Acquisition Data Analysis Workflows.” Journal of Proteome
Research 23 (6): 2078–89.
https://doi.org/10.1021/acs.jproteome.4c00048.
Sticker, Adriaan, Ludger Goeminne, Lennart Martens, and Lieven Clement.
2020. “Robust Summarization and Inference in Proteome-Wide
Label-Free Quantification.” Mol. Cell. Proteomics 19
(7): 1209–19.
Vandenbulcke, Stijn, Christophe Vanderaa, Oliver Crook, Lennart Martens,
and Lieven Clement. 2025. “Msqrob2TMT: Robust Linear
Mixed Models for Inferring Differential Abundant Proteins in Labeled
Experiments with Arbitrarily Complex Design.” Mol. Cell.
Proteomics 24 (7): 101002.