Mass spectrometry-untargeted proteomic data analysis software tools

A number of technologies can be used to study proteomes, but arguably none is more powerful than mass spectrometry (MS; Aebersold and Mann, 2003; Cravatt et al., 2007; Domon and Aebersold, 2010). There are two fundamentally different MS-based strategies for analyzing proteomes: discovery-based identification and targeted quantification (Doerr, 2013; Picotti and Aebersold, 2012). With a discovery-based strategy, the goal is usually to identify as many proteins as possible. The goal of a targeted proteomics experiment is to monitor a select few proteins of interest with high sensitivity, reproducibility and quantitative accuracy.

Data preprocessing

Data processing


Data analysis

Data visualization

Enrichment analysis


File manipulation


Unclassified tools