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Computational analysis for mass spectrometry-based proteomics data

DIA-Umpire is an open source Java program for computational analysis of data independent acquisition (DIA) mass spectrometry-based proteomics data. It enables untargeted peptide and protein identification and quantitation using DIA data, and also incorporates targeted extraction to reduce the number of cases of missing quantitation.

Four Major Modules

Suggested workflow

Depending on the scale of applications, three application scenarios which require different combinations of DIA-Umpire modules are described in our user guides.

  1. Identification only analysis (Steps A->B)

  2. Small scale identification and quantitation analysis with minimal computational costs (Steps A->B->D)

  3. Complete DIA-Umpire identification and quantitation analysis (Steps A->B->C->D)

System Requirement

DIA-Umpire is written in Java, which is cross operating system programming language. To execute DIA-Umpire, Java 7 or higher (download link:Java SE Runtime Environment 7) version is required. As a rule of thumb, it is recommended have at least double the amount of RAM as the average size of your mzXML files (mzXML written in 32-bit format without zlib compression). If mzXML is in 64-bit format, then RAM requirements should be approximately the size of the file.

Other Usages


The first step of DIA-Umpire analysis. It is a signal extraction module to generate pseudo MS/MS spectra given a DIA file


Main DIA-Umpire class libraries


DDA-based MS1 quantification tool based on the feature detection algorithm.