Kelsi Caywood, Gary L Darmstadt
Gender mainstreaming at 25 years: Toward an inclusive, collaborative, and structured research agenda
Journal of global health
identification differentially expressed proteins proteomics workflow typically encompasses five key steps raw data quantification expression matrix construction matrix normalization missing value imputation mvi differential expression analysis plethora options step makes challenging identify optimal workflows maximize identification differentially expressed proteins identify optimal workflows common properties conduct extensive study involving 34576 combinatoric experiments 24 gold standard spikein datasets applying frequent pattern mining techniques topranked workflows uncover highperforming rules demonstrate optimality conserved properties via machine learning confirm optimal workflows indeed predictable average crossvalidation f1 scores matthews correlation coefficients surpassing 084 introduce ensemble inference integrate results individual topperforming workflows expanding differential proteome coverage resolve inconsistencies ensemble inference provides gains pauc 461 gmean 1114 facilitates effective aggregation information across varied quantification approaches topn directlfq maxlfq intensities spectral counts however development evaluation needed establish acceptable frameworks conducting ensemble inference multiple proteomics workflows