biostudies-literatureOchoteco Asensio JSeventh Framework Programme2057-2069https://www.ebi.ac.uk/biostudies/studies/S-EPMC9077535biostudies-literatureUnknown20Proteins are often considered the main biological element in charge of the different functions and structures of a cell. However, proteomics, the global study of all expressed proteins, often performed by mass spectrometry, is limited by its stochastic sampling and can only quantify a limited amount of protein per sample. Transcriptomics, which allows an exhaustive analysis of all expressed transcripts, is often used as a surrogate. However, the transcript level does not present a high level of correlation with the corresponding protein level, notably due to the existence of several post-transcriptional regulatory mechanisms. In this publication, we hypothesize that the missing protein values in proteomics could be predicted using machine learning regression methods, trained with many featComputational and structural biotechnology journalPredicting missing proteomics values using machine learning: Filling the gap using transcriptomics and other biological features.PMC9077535602156Caiment FOchoteco Asensio JVerheijen MfalsePredicting missing proteomics values using machine learning: Filling the gap using transcriptomics and other biological features.Proteins are often considered the main biological element in charge of the different functions and structures of a cell. However, proteomics, the global study of all expressed proteins, often performed by mass spectrometry, is limited by its stochastic sampling and can only quantify a limited amount of protein per sample. Transcriptomics, which allows an exhaustive analysis of all expressed transcripts, is often used as a surrogate. However, the transcript level does not present a high level of correlation with the corresponding protein level, notably due to the existence of several post-transcriptional regulatory mechanisms. In this publication, we hypothesize that the missing protein values in proteomics could be predicted using machine learning regression methods, trained with many feat2022-01-01T00:00:00Z20222026-05-31T20:59:43.847Z2025-02-19T04:21:03.794ZS-EPMC90775353560196010.1016/j.csbj.2022.04.017