refs.bib

@article{Fabregat2017,
  doi = {10.1093/nar/gkx1132},
  url = {https://doi.org/10.1093/nar/gkx1132},
  year = {2017},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {46},
  number = {D1},
  pages = {D649--D655},
  author = {Antonio Fabregat and Steven Jupe and Lisa Matthews and Konstantinos Sidiropoulos and Marc Gillespie and Phani Garapati and Robin Haw and Bijay Jassal and Florian Korninger and Bruce May and Marija Milacic and Corina Duenas Roca and Karen Rothfels and Cristoffer Sevilla and Veronica Shamovsky and Solomon Shorser and Thawfeek Varusai and Guilherme Viteri and Joel Weiser and Guanming Wu and Lincoln Stein and Henning Hermjakob and Peter D'Eustachio},
  title = {The Reactome Pathway Knowledgebase},
  journal = {Nucleic Acids Research}
}

@article{Chawade2014,
  doi = {10.1021/pr401264n},
  url = {https://doi.org/10.1021/pr401264n},
  year = {2014},
  month = may,
  publisher = {American Chemical Society ({ACS})},
  volume = {13},
  number = {6},
  pages = {3114--3120},
  author = {Aakash Chawade and Erik Alexandersson and Fredrik Levander},
  title = {Normalyzer: A Tool for Rapid Evaluation of Normalization Methods for Omics Data Sets},
  journal = {Journal of Proteome Research}
}

@article{PinaJimnez2021,
  doi = {10.3390/ijms221910516},
  url = {https://doi.org/10.3390/ijms221910516},
  year = {2021},
  month = sep,
  publisher = {{MDPI} {AG}},
  volume = {22},
  number = {19},
  pages = {10516},
  author = {Emmanuel Pina-Jim{\'{e}}nez and Fernando Calzada and Elih{\'{u}} Bautista and Rosa Mar{\'{\i}}a Ordo{\~{n}}ez-Razo and Claudia Vel{\'{a}}zquez and Elizabeth Barbosa and Normand Garc{\'{\i}}a-Hern{\'{a}}ndez},
  title = {Incomptine A Induces Apoptosis,  {ROS} Production and a Differential Protein Expression on Non-Hodgkin's Lymphoma Cells},
  journal = {International Journal of Molecular Sciences}
}

@article{AmiriDashatan2021,
  doi = {10.1016/j.cimid.2021.101617},
  url = {https://doi.org/10.1016/j.cimid.2021.101617},
  year = {2021},
  month = apr,
  publisher = {Elsevier {BV}},
  volume = {75},
  pages = {101617},
  author = {Nasrin Amiri-Dashatan and Nayebali Ahmadi and Mostafa Rezaei-Tavirani and Mehdi Koushki},
  title = {Identification of differential protein expression and putative drug target in metacyclic stage of Leishmania major and Leishmania tropica: A quantitative proteomics and computational view},
  journal = {Comparative Immunology,  Microbiology and Infectious Diseases}
}

@article{Anitua2018,
  doi = {10.1371/journal.pone.0205073},
  url = {https://doi.org/10.1371/journal.pone.0205073},
  year = {2018},
  month = oct,
  publisher = {Public Library of Science ({PLoS})},
  volume = {13},
  number = {10},
  pages = {e0205073},
  author = {Eduardo Anitua and Mar{\'{\i}}a de la Fuente and Francisco Muruzabal and Ronald Mauricio S{\'{a}}nchez-{\'{A}}vila and Jes{\'{u}}s Merayo-Lloves and Mikel Azkargorta and Felix Elortza and Gorka Orive},
  editor = {Alfred S. Lewin},
  title = {Differential profile of protein expression on human keratocytes treated with autologous serum and plasma rich in growth factors ({PRGF})},
  journal = {{PLOS} {ONE}}
}

@article{Sticker2020,
  doi = {10.1074/mcp.ra119.001624},
  url = {https://doi.org/10.1074/mcp.ra119.001624},
  year = {2020},
  month = jul,
  publisher = {Elsevier {BV}},
  volume = {19},
  number = {7},
  pages = {1209--1219},
  author = {Adriaan Sticker and Ludger Goeminne and Lennart Martens and Lieven Clement},
  title = {Robust Summarization and Inference in Proteome-wide Label-free Quantification},
  journal = {Molecular and Cellular Proteomics}
}

@article{Ritchie2015,
  doi = {10.1093/nar/gkv007},
  url = {https://doi.org/10.1093/nar/gkv007},
  year = {2015},
  month = jan,
  publisher = {Oxford University Press ({OUP})},
  volume = {43},
  number = {7},
  pages = {e47--e47},
  author = {Matthew E. Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W. Law and Wei Shi and Gordon K. Smyth},
  title = {limma powers differential expression analyses for {RNA}-sequencing and microarray studies},
  journal = {Nucleic Acids Research}
}

@article{McAlister2014,
  doi = {10.1021/ac502040v},
  url = {https://doi.org/10.1021/ac502040v},
  year = {2014},
  month = jul,
  publisher = {American Chemical Society ({ACS})},
  volume = {86},
  number = {14},
  pages = {7150--7158},
  author = {Graeme C. McAlister and David P. Nusinow and Mark P. Jedrychowski and Martin W\"{u}hr and Edward L. Huttlin and Brian K. Erickson and Ramin Rad and Wilhelm Haas and Steven P. Gygi},
  title = {{MultiNotch} {MS}3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes},
  journal = {Analytical Chemistry}
}

@article{Ting2011,
  doi = {10.1038/nmeth.1714},
  url = {https://doi.org/10.1038/nmeth.1714},
  year = {2011},
  month = oct,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {8},
  number = {11},
  pages = {937--940},
  author = {Lily Ting and Ramin Rad and Steven P Gygi and Wilhelm Haas},
  title = {{MS}3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics},
  journal = {Nature Methods}
}

@article{Frankenfield2022,
  doi = {10.1021/acs.jproteome.2c00145},
  url = {https://doi.org/10.1021/acs.jproteome.2c00145},
  year = {2022},
  month = jul,
  publisher = {American Chemical Society ({ACS})},
  volume = {21},
  number = {9},
  pages = {2104--2113},
  author = {Ashley M. Frankenfield and Jiawei Ni and Mustafa Ahmed and Ling Hao},
  title = {Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for {DDA} and {DIA} Proteomics},
  journal = {Journal of Proteome Research}
}

@article{Law2014,
  doi = {10.1186/gb-2014-15-2-r29},
  url = {https://doi.org/10.1186/gb-2014-15-2-r29},
  year = {2014},
  publisher = {Springer Science and Business Media {LLC}},
  volume = {15},
  number = {2},
  pages = {R29},
  author = {Charity W Law and Yunshun Chen and Wei Shi and Gordon K Smyth},
  title = {voom: precision weights unlock linear model analysis tools for {RNA}-seq read counts},
  journal = {Genome Biology}
}

@article{Kll2007,
  doi = {10.1038/nmeth1113},
  url = {https://doi.org/10.1038/nmeth1113},
  year = {2007},
  month = oct,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {4},
  number = {11},
  pages = {923--925},
  author = {Lukas K\"{a}ll and Jesse D Canterbury and Jason Weston and William Stafford Noble and Michael J MacCoss},
  title = {Semi-supervised learning for peptide identification from shotgun proteomics datasets},
  journal = {Nature Methods}
}

@article{Smyth2004,
  doi = {10.2202/1544-6115.1027},
  url = {https://doi.org/10.2202/1544-6115.1027},
  year = {2004},
  month = jan,
  publisher = {Walter de Gruyter {GmbH}},
  volume = {3},
  number = {1},
  pages = {1--25},
  author = {Gordon K Smyth},
  title = {Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments},
  journal = {Statistical Applications in Genetics and Molecular Biology}
}

@article{Huber2015,
  doi = {10.1038/nmeth.3252},
  url = {https://doi.org/10.1038/nmeth.3252},
  year = {2015},
  month = jan,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {12},
  number = {2},
  pages = {115--121},
  author = {Wolfgang Huber and Vincent J Carey and Robert Gentleman and Simon Anders and Marc Carlson and Benilton S Carvalho and Hector Corrada Bravo and Sean Davis and Laurent Gatto and Thomas Girke and Raphael Gottardo and Florian Hahne and Kasper D Hansen and Rafael A Irizarry and Michael Lawrence and Michael I Love and James MacDonald and Valerie Obenchain and Andrzej K Ole{\'{s}} and Herv{\'{e}} Pag{\`{e}}s and Alejandro Reyes and Paul Shannon and Gordon K Smyth and Dan Tenenbaum and Levi Waldron and Martin Morgan},
  title = {Orchestrating high-throughput genomic analysis with Bioconductor},
  journal = {Nature Methods}
}

@Manual{Rstat,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
    address = {Vienna, Austria},
    year = {2011},
    note = {{ISBN} 3-900051-07-0},
    url = {http://www.R-project.org/},
}

@article{Plubell2017,
  doi = {10.1074/mcp.m116.065524},
  url = {https://doi.org/10.1074/mcp.m116.065524},
  year = {2017},
  month = may,
  publisher = {Elsevier {BV}},
  volume = {16},
  number = {5},
  pages = {873--890},
  author = {Deanna L. Plubell and Phillip A. Wilmarth and Yuqi Zhao and Alexandra M. Fenton and Jessica Minnier and Ashok P. Reddy and John Klimek and Xia Yang and Larry L. David and Nathalie Pamir},
  title = {Extended Multiplexing of Tandem Mass Tags ({TMT}) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue},
  journal = {Molecular and Cellular Proteomics}
}

@article{Choi2014,
  doi = {10.1093/bioinformatics/btu305},
  url = {https://doi.org/10.1093/bioinformatics/btu305},
  year = {2014},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {30},
  number = {17},
  pages = {2524--2526},
  author = {Meena Choi and Ching-Yun Chang and Timothy Clough and Daniel Broudy and Trevor Killeen and Brendan MacLean and Olga Vitek},
  title = {{MSstats}: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments},
  journal = {Bioinformatics}
}

@article{Huang2020,
  doi = {10.1074/mcp.ra120.002105},
  url = {https://doi.org/10.1074/mcp.ra120.002105},
  year = {2020},
  month = oct,
  publisher = {Elsevier {BV}},
  volume = {19},
  number = {10},
  pages = {1706--1723},
  author = {Ting Huang and Meena Choi and Manuel Tzouros and Sabrina Golling and Nikhil Janak Pandya and Balazs Banfai and Tom Dunkley and Olga Vitek},
  title = {{MSstatsTMT}: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures},
  journal = {Molecular and Cellular Proteomics}
}

@article{Goeminne2020,
  doi = {10.1021/acs.analchem.9b04375},
  url = {https://doi.org/10.1021/acs.analchem.9b04375},
  year = {2020},
  month = mar,
  publisher = {American Chemical Society ({ACS})},
  volume = {92},
  number = {9},
  pages = {6278--6287},
  author = {Ludger J. E. Goeminne and Adriaan Sticker and Lennart Martens and Kris Gevaert and Lieven Clement},
  title = {{MSqRob} Takes the Missing Hurdle: Uniting Intensity- and Count-Based Proteomics},
  journal = {Analytical Chemistry}
}

@article{Ranathunge2022,
  doi = {10.1101/2022.08.17.503867},
  url = {https://doi.org/10.1101/2022.08.17.503867},
  year = {2022},
  month = aug,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Chathurani Ranathunge and Sagar S. Patel and Lubna Pinky and Vanessa L. Correll and Shimin Chen and O. John Semmes and Robert K. Armstrong and C. Donald Combs and Julius O. Nyalwidhe},
  title = {promor: a comprehensive R package for label-free proteomics data analysis and predictive modeling}
}

@article{Gierlinski2018,
  doi = {10.1101/416511},
  url = {https://doi.org/10.1101/416511},
  year = {2018},
  month = sep,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Marek Gierlinski and Francesco Gastaldello and Chris Cole and Geoffrey J. Barton},
  title = {Proteus: an R package for downstream analysis of {MaxQuant} output}
}

@article{Quast2021,
  doi = {10.1093/bioadv/vbab041},
  url = {https://doi.org/10.1093/bioadv/vbab041},
  year = {2021},
  month = dec,
  publisher = {Oxford University Press ({OUP})},
  volume = {2},
  number = {1},
  author = {Jan-Philipp Quast and Dina Schuster and Paola Picotti},
  editor = {Cecilia Arighi},
  title = {protti: an R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data},
  journal = {Bioinformatics Advances}
}

@article{Wolski2022,
  doi = {10.1101/2022.06.07.494524},
  url = {https://doi.org/10.1101/2022.06.07.494524},
  year = {2022},
  month = jun,
  publisher = {Cold Spring Harbor Laboratory},
  author = {Witold E. Wolski and Paolo Nanni and Jonas Grossmann and Maria d'Errico and Ralph Schlapbach and Christian Panse},
  title = {prolfqua: A Comprehensive R-package for Proteomics Differential Expression Analysis}
}

@article{FernndezCosta2020,
  doi = {10.1021/acs.jproteome.0c00153},
  url = {https://doi.org/10.1021/acs.jproteome.0c00153},
  year = {2020},
  month = jun,
  publisher = {American Chemical Society ({ACS})},
  volume = {19},
  number = {8},
  pages = {3153--3161},
  author = {Carolina Fern{\'{a}}ndez-Costa and Salvador Mart{\'{\i}}nez-Bartolom{\'{e}} and Daniel B. McClatchy and Anthony J. Saviola and Nam-Kyung Yu and John R. Yates},
  title = {Impact of the Identification Strategy on the Reproducibility of the {DDA} and {DIA} Results},
  journal = {Journal of Proteome Research}
}

@article{Hu2016,
  doi = {10.12688/f1000research.7042.1},
  url = {https://doi.org/10.12688/f1000research.7042.1},
  year = {2016},
  month = mar,
  publisher = {F1000 Research Ltd},
  volume = {5},
  pages = {419},
  author = {Alex Hu and William S. Noble and Alejandro Wolf-Yadlin},
  title = {Technical advances in proteomics: new developments in data-independent acquisition},
  journal = {F1000Research}
}

@article{Dupree2020,
  doi = {10.3390/proteomes8030014},
  url = {https://doi.org/10.3390/proteomes8030014},
  year = {2020},
  month = jul,
  publisher = {{MDPI} {AG}},
  volume = {8},
  number = {3},
  pages = {14},
  author = {Emmalyn J. Dupree and Madhuri Jayathirtha and Hannah Yorkey and Marius Mihasan and Brindusa Alina Petre and Costel C. Darie},
  title = {A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field},
  journal = {Proteomes}
}

@incollection{Obermaier2015,
  doi = {10.1007/978-1-4939-2550-6_13},
  url = {https://doi.org/10.1007/978-1-4939-2550-6_13},
  year = {2015},
  publisher = {Springer New York},
  pages = {153--165},
  author = {Christian Obermaier and Anja Griebel and Reiner Westermeier},
  title = {Principles of Protein Labeling Techniques},
  booktitle = {Methods in Molecular Biology}
}

@article{Goeminne2016,
  doi = {10.1074/mcp.m115.055897},
  url = {https://doi.org/10.1074/mcp.m115.055897},
  year = {2016},
  month = feb,
  publisher = {Elsevier {BV}},
  volume = {15},
  number = {2},
  pages = {657--668},
  author = {Ludger J. E. Goeminne and Kris Gevaert and Lieven Clement},
  title = {Peptide-level Robust Ridge Regression Improves Estimation,  Sensitivity,  and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics},
  journal = {Molecular and Cellular Proteomics}
}

@article{Phipson2016,
  doi = {10.1214/16-aoas920},
  url = {https://doi.org/10.1214/16-aoas920},
  year = {2016},
  month = jun,
  publisher = {Institute of Mathematical Statistics},
  volume = {10},
  number = {2},
  author = {Belinda Phipson and Stanley Lee and Ian J. Majewski and Warren S. Alexander and Gordon K. Smyth},
  title = {Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression},
  journal = {The Annals of Applied Statistics}
}

@article{Yu2016,
  doi = {10.1039/c5mb00663e},
  url = {https://doi.org/10.1039/c5mb00663e},
  year = {2016},
  publisher = {Royal Society of Chemistry ({RSC})},
  volume = {12},
  number = {2},
  pages = {477--479},
  author = {Guangchuang Yu and Qing-Yu He},
  title = {{ReactomePA}: an R/Bioconductor package for reactome pathway analysis and visualization},
  journal = {Molecular {BioSystems}}
}

@article{Wu2021,
  doi = {10.1016/j.xinn.2021.100141},
  url = {https://doi.org/10.1016/j.xinn.2021.100141},
  year = {2021},
  month = aug,
  publisher = {Elsevier {BV}},
  volume = {2},
  number = {3},
  pages = {100141},
  author = {Tianzhi Wu and Erqiang Hu and Shuangbin Xu and Meijun Chen and Pingfan Guo and Zehan Dai and Tingze Feng and Lang Zhou and Wenli Tang and Li Zhan and Xiaocong Fu and Shanshan Liu and Xiaochen Bo and Guangchuang Yu},
  title = {{clusterProfiler} 4.0: A universal enrichment tool for interpreting omics data},
  journal = {The Innovation}
}

@Manual{enrichplot,
  author = {Guangchuang Yu},
  year = {2022},
  title = {enrichplot: Visualization of Functional Enrichment Result},
  note = {R package version 1.18.3}
}

@article{Eden2009,
  doi = {10.1186/1471-2105-10-48},
  url = {https://doi.org/10.1186/1471-2105-10-48},
  year = {2009},
  month = feb,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {10},
  number = {1},
  author = {Eran Eden and Roy Navon and Israel Steinfeld and Doron Lipson and Zohar Yakhini},
  title = {{GOrilla}: a tool for discovery and visualization of enriched {GO} terms in ranked gene lists},
  journal = {{BMC} Bioinformatics}
}

@article{Mi2012,
  doi = {10.1093/nar/gks1118},
  url = {https://doi.org/10.1093/nar/gks1118},
  year = {2012},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {41},
  number = {D1},
  pages = {D377--D386},
  author = {Huaiyu Mi and Anushya Muruganujan and Paul D. Thomas},
  title = {{PANTHER} in 2013: modeling the evolution of gene function,  and other gene attributes,  in the context of phylogenetic trees},
  journal = {Nucleic Acids Research}
}

@article{Thomas2021,
  doi = {10.1002/pro.4218},
  url = {https://doi.org/10.1002/pro.4218},
  year = {2021},
  month = nov,
  publisher = {Wiley},
  volume = {31},
  number = {1},
  pages = {8--22},
  author = {Paul D. Thomas and Dustin Ebert and Anushya Muruganujan and Tremayne Mushayahama and Laurent-Philippe Albou and Huaiyu Mi},
  title = {{PANTHER}: Making genome-scale phylogenetics accessible to all},
  journal = {Protein Science}
}


@article{Willforss2018,
  doi = {10.1021/acs.jproteome.8b00523},
  url = {https://doi.org/10.1021/acs.jproteome.8b00523},
  year = {2018},
  month = oct,
  publisher = {American Chemical Society ({ACS})},
  volume = {18},
  number = {2},
  pages = {732--740},
  author = {Jakob Willforss and Aakash Chawade and Fredrik Levander},
  title = {{NormalyzerDE}: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis},
  journal = {Journal of Proteome Research}
}

@Manual{biostrings, 
  author = {H. Pages and P. Aboyoun and R. Gentleman and S. {DebRoy}},
  title = {Biostrings: Efficient Manipulation of Biological Strings},
  year = {2022},
  note = {R package version 2.66.0}
}

@Manual{topGO, 
  author = {Adrian Alexa},
  title = {{topGO}: Enrichment Analysis for Gene Ontology},
  year = {2022},
  note = {R package version 2.50.0}
}

@Manual{GofuncR,
  author = {Steffi Grote},
  title = {{GOfuncR}: Gene ontology enrichment using {FUNC}},
  year = {2022},
  note = {R package version 1.18.0}
}

@article{Gatto2011,
  doi = {10.1093/bioinformatics/btr645},
  url = {https://doi.org/10.1093/bioinformatics/btr645},
  year = {2011},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {28},
  number = {2},
  pages = {288--289},
  author = {Laurent Gatto and Kathryn S. Lilley},
  title = {{MSnbase}-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization,  processing and quantitation},
  journal = {Bioinformatics}
}

@article{Gatto2020,
  doi = {10.1021/acs.jproteome.0c00313},
  url = {https://doi.org/10.1021/acs.jproteome.0c00313},
  year = {2020},
  month = sep,
  publisher = {American Chemical Society ({ACS})},
  volume = {20},
  number = {1},
  pages = {1063--1069},
  author = {Laurent Gatto and Sebastian Gibb and Johannes Rainer},
  title = {{MSnbase},  Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data},
  journal = {Journal of Proteome Research}
}

@article{Rainer2022,
  doi = {10.3390/metabo12020173},
  url = {https://doi.org/10.3390/metabo12020173},
  year = {2022},
  month = feb,
  publisher = {{MDPI} {AG}},
  volume = {12},
  number = {2},
  pages = {173},
  author = {Johannes Rainer and Andrea Vicini and Liesa Salzer and Jan Stanstrup and Josep M. Badia and Steffen Neumann and Michael A. Stravs and Vinicius Verri Hernandes and Laurent Gatto and Sebastian Gibb and Michael Witting},
  title = {A modular and expandable ecosystem for metabolomics data annotation in R},
  journal = {Metabolites}
}

@Manual{HutchingsData,
    title = {A Bioconductor workflow for processing, evaluating and interpreting expression proteomics data},
    author = {Charlotte Hutchings and Charlotte Dawson and Thomas Krueger and Kathryn Lilley and and Lisa Breckels},
    publisher = {Zenodo},
    year = {2023},
    doi = {10.5281/ZENODO.7837375},
    url = {https://zenodo.org/record/7837375}
}


@Manual{QFeat,
    title = {{QFeatures}: Quantitative features for mass spectrometry data},
    author = {Laurent Gatto and Christophe Vanderaa},
    year = {2023},
    note = {R package version 1.9.2},
    url = {https://github.com/RforMassSpectrometry/QFeatures}
}

@Manual{SumExp,
    title = {{SummarizedExperiment}: {SummarizedExperiment} container},
    author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
    year = {2022},
    note = {R package version 1.29.1},
    url = {https://bioconductor.org/packages/SummarizedExperiment}
}

@Manual{p_val, 
  author = {David Robinson},
  title = {How to interpret a p-value histogram},
  year = {2014},
  url = {http://varianceexplained.org/statistics/interpreting-pvalue-histogram/}
}
  
@article{ORourke2019,
  doi = {10.3390/proteomes7030029},
  url = {https://doi.org/10.3390/proteomes7030029},
  year = {2019},
  month = aug,
  publisher = {{MDPI} {AG}},
  volume = {7},
  number = {3},
  pages = {29},
  author = {Matthew B. O'Rourke and Stephanie E. L. Town and Penelope V. Dalla and Fiona Bicknell and Naomi Koh Belic and Jake P. Violi and Joel R. Steele and Matthew P. Padula},
  title = {What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows},
  journal = {Proteomes}
}

@article{Darbani2014,
  doi = {10.1186/2241-5793-21-3},
  url = {https://doi.org/10.1186/2241-5793-21-3},
  year = {2014},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {21},
  number = {1},
  author = {Behrooz Darbani and Charles Neal Stewart},
  title = {Reproducibility and reliability assays of the gene expression-measurements},
  journal = {Journal of Biological Research-Thessaloniki}
}

@Manual{simply_stats, 
  author = {Rafael Irizarry},
  title = {Correlation is not a measure of reproducibility},
  year = {2015},
  url = {https://simplystatistics.org/posts/2015-08-12-correlation-is-not-a-measure-of-reproducibility/}
}

@article{Bunting2019,
  doi = {10.1016/j.echo.2019.08.015},
  url = {https://doi.org/10.1016/j.echo.2019.08.015},
  year = {2019},
  month = dec,
  publisher = {Elsevier {BV}},
  volume = {32},
  number = {12},
  pages = {1505--1515},
  author = {Karina V. Bunting and Richard P. Steeds and Luke T. Slater and Jennifer K. Rogers and Georgios V. Gkoutos and Dipak Kotecha},
  title = {A Practical Guide to Assess the Reproducibility of Echocardiographic Measurements},
  journal = {Journal of the American Society of Echocardiography}
}

@article{Wolski2023,
  doi = {10.1021/acs.jproteome.2c00441},
  url = {https://doi.org/10.1021/acs.jproteome.2c00441},
  year = {2023},
  month = mar,
  publisher = {American Chemical Society ({ACS})},
  volume = {22},
  number = {4},
  pages = {1092--1104},
  author = {Witold E. Wolski and Paolo Nanni and Jonas Grossmann and Maria d'Errico and Ralph Schlapbach and Christian Panse},
  title = {prolfqua: A Comprehensive {R}-Package for Proteomics Differential Expression Analysis},
  journal = {Journal of Proteome Research}
}

@article{PerezRiverol2021,
  doi = {10.1093/nar/gkab1038},
  url = {https://doi.org/10.1093/nar/gkab1038},
  year = {2021},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {50},
  number = {D1},
  pages = {D543--D552},
  author = {Yasset Perez-Riverol and Jingwen Bai and Chakradhar Bandla and David Garc{\'{\i}}a-Seisdedos and Suresh Hewapathirana and Selvakumar Kamatchinathan and Deepti Kundu and Ananth Prakash and Anika Frericks-Zipper and Martin Eisenacher and Mathias Walzer and Shengbo Wang and Alvis Brazma and Juan Antonio Vizca{\'{\i}}no},
  title = {The {PRIDE} database resources in 2022: a hub for mass spectrometry-based proteomics evidences},
  journal = {Nucleic Acids Research}
}

@article{Deutsch2022,
  doi = {10.1093/nar/gkac1040},
  url = {https://doi.org/10.1093/nar/gkac1040},
  year = {2022},
  month = nov,
  publisher = {Oxford University Press ({OUP})},
  volume = {51},
  number = {D1},
  pages = {D1539--D1548},
  author = {Eric W Deutsch and Nuno Bandeira and Yasset Perez-Riverol and Vagisha Sharma and Jeremy Carver and Luis Mendoza and Deepti J Kundu and Shengbo Wang and Chakradhar Bandla and Selvakumar Kamatchinathan and Suresh Hewapathirana and Benjamin Pullman and Julie Wertz and Zhi Sun and Shin Kawano and Shujiro Okuda and Yu Watanabe and Brendan MacLean and Michael MacCoss and Yunping Zhu and Yasushi Ishihama and Juan Antonio Vizca{\'{\i}}no},
  title = {The {ProteomeXchange} consortium at 10 years: 2023 update},
  journal = {Nucleic Acids Research}
}

@article{Leek2010,
  doi = {10.1038/nrg2825},
  url = {https://doi.org/10.1038/nrg2825},
  year = {2010},
  month = sep,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {11},
  number = {10},
  pages = {733--739},
  author = {Jeffrey T. Leek and Robert B. Scharpf and H{\'{e}}ctor Corrada Bravo and David Simcha and Benjamin Langmead and W. Evan Johnson and Donald Geman and Keith Baggerly and Rafael A. Irizarry},
  title = {Tackling the widespread and critical impact of batch effects in high-throughput data},
  journal = {Nature Reviews Genetics}
}

@article{BH1995,
  doi = {10.1111/j.2517-6161.1995.tb02031.x},
  year = {1995},
  publisher = {Oxford University Press},
  volume = {57},
  number = {1},
  pages = {289--300},
  author = {Yoav Benjamini and Yosef Hochberg},
  title = {Controlling the false discovery rate: a practical and powerful approach to multiple testing},
  journal = {Journal of Royal Statistical Society}
}

@article{Liu2021,
  doi = {10.1093/bib/bbaa112},
  url = {https://doi.org/10.1093/bib/bbaa112},
  year = {2021},
  month = jun,
  publisher = {Oxford University Press ({OUP})},
  volume = {22},
  number = {3},
  author = {Mingyi Liu and Ashok Dongre},
  title = {Proper imputation of missing values in proteomics datasets for differential expression analysis},
  journal = {Briefings in Bioinformatics}
}

@article{Lazar2016,
  doi = {10.1021/acs.jproteome.5b00981},
  url = {https://doi.org/10.1021/acs.jproteome.5b00981},
  year = {2016},
  month = mar,
  publisher = {American Chemical Society ({ACS})},
  volume = {15},
  number = {4},
  pages = {1116--1125},
  author = {Cosmin Lazar and Laurent Gatto and Myriam Ferro and Christophe Bruley and Thomas Burger},
  title = {Accounting for the multiple natures of missing salues in label-free quantitative proteomics data sets to compare imputation strategies},
  journal = {Journal of Proteome Research}
}

@article{Karpievitch2009,
  doi = {10.1093/bioinformatics/btp362},
  url = {https://doi.org/10.1093/bioinformatics/btp362},
  year = {2009},
  month = jun,
  publisher = {Oxford University Press ({OUP})},
  volume = {25},
  number = {16},
  pages = {2028--2034},
  author = {Yuliya Karpievitch and Jeff Stanley and Thomas Taverner and Jianhua Huang and Joshua N. Adkins and Charles Ansong and Fred Heffron and Thomas O. Metz and Wei-Jun Qian and Hyunjin Yoon and Richard D. Smith and Alan R. Dabney},
  title = {A statistical framework for protein quantitation in bottom-up {MS}-based proteomics},
  journal = {Bioinformatics}
}

@article{Brenes2019,
  doi = {10.1074/mcp.ra119.001472},
  url = {https://doi.org/10.1074/mcp.ra119.001472},
  year = {2019},
  month = oct,
  publisher = {Elsevier {BV}},
  volume = {18},
  number = {10},
  pages = {1967--1980},
  author = {Alejandro Brenes and Jens Hukelmann and Dalila Bensaddek and Angus Lamond},
  title = {Multibatch {TMT} reveals false positives, batch effects and missing values},
  journal = {Molecular and Cellular Proteomics}
}

@article{Zhu2020,
  title = {DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis},
  volume = {19},
  ISSN = {1535-9476},
  url = {http://dx.doi.org/10.1074/mcp.TIR119.001646},
  DOI = {10.1074/mcp.tir119.001646},
  number = {6},
  journal = {Molecular and Cellular Proteomics},
  publisher = {Elsevier BV},
  author = {Zhu,  Yafeng and Orre,  Lukas M. and Zhou Tran,  Yan and Mermelekas,  Georgios and Johansson,  Henrik J. and Malyutina,  Alina and Anders,  Simon and Lehti\"{o},  Janne},
  year = {2020},
  month = jun,
  pages = {1047–1057}
}