The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

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The PRIDE database and related tools and resources in 2019: improving support for quantification data (2018, positive): “All PRIDE integrated proteomics datasets were manually curated and re-analyzed using a MaxQuant based pipeline.”
Expression Atlas: gene and protein expression across multiple studies and organisms (2017, methodology): “Proteomics data are currently processed in custom-designed way for each data set, using open source and/or free to use software such as OpenMS (20) and MaxQuant (21).”
IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs (2020, methodology): “To address the missing value problem in DDA-based proteomics, a number of “identification transfer” approaches have been devised (10–13), exemplified by the matchbetween-runs (MBR) option in MaxQuant (14, 15) that allows “transfer” of identified precursor peptide peaks from one run (referred to belo”
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation (2017, methodology): “MaxQuant searches were performed using the standard work flow [47].”