1. Unveiling the Links between Peptide Identification and Differential Analysis FDR Controls by Means of a Practical Introduction to Knockoff Filters
Lucas Etourneau, Nelle Varoquaux, and Thomas Burger
2. A Pipeline for Peptide Detection Using Multiple Decoys
Syamand Hasam, Kristen Emery, William Stafford Noble, and Uri Keich
3. Enhanced Proteomic Data Analysis with MetaMorpheus
Rachel M. Miller, Robert J. Millikin, Zach Rolfs, Michael R. Shortreed, and Lloyd
M. Smith
4. Validation of MS/MS Identifications and Label-Free Quantification Using Proline
V ronique Dupierris, Anne-Marie Hesse, Jean-Philippe Menetrey, David Bouyssi , Thomas Burger, Yohann Cout , and Christophe Bruley
5. Integrating Identification and Quantification Uncertainty for Differential Protein Abundance Analysis with Triqler
Matthew The and Lukas K ll
6. Left-Censored Missing Value Imputation Approach for MS-Based Proteomics Data with Gsimp
Runmin Wei and Jingye Wang
7. Towards a More Accurate Differential Analysis of Multiple Imputed Proteomics Data with mi4limma
Marie Chion, Christine Carapito, and Fr d ric Bertrand
8. Uncertainty Aware Protein-Level Quantification and Differential Expression Analysis of Proteomics Data with seaMass
Alexander M. Phillips, Richard D. Unwin, Simon J. Hubbard, and Andrew W. Dowsey
9. Statistical Analysis of Quantitative Peptidomics and Peptide-Level Proteomics Data with Prostar
Marianne Tardif, Enora Fremy, Anne-Marie Hesse, Thomas Burger, Yohann Cout , and Samuel Wieczorek
10. msmsEDA and msmsTests: Label-Free Differential Expression by Spectral Counts
Josep Gregori, lex S nchez, and Josep Villanueva
11. Exploring Protein Interactome Data with IPinquiry: Statistical Analysis and Data Visualization by Spectral Counts
Lauriane Kuhn, Timoth e Vincent, Philippe Hammann, and H l ne Zuber
12. Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells
Quentin Giai Gianetto
13. Fast, Free, and Flexible Peptide and Protein Quantification with FlashLFQ
Robert J. Millikin, Michael R. Shortreed, Mark Scalf, and Lloyd M. Smith
14. Robust Prediction and Protein Selection with Adaptive PENSE
David Kepplinger and Gabriela V. Cohen Freue
15. Multivariate Analysis with the R Package mixOmics
Zoe Welham, S bastien D jean, and Kim-Anh L Cao
16. Inte