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Nesvilab · Jan 4, 2021 · a6ffb67 · a6ffb67
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-IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies.
+IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of [FragPipe](http://fragpipe.nesvilab.org/) (recommended option), but can also be run as a command-line tool.  
 
 ### Workflow of peak tracing and quantification
 <img src="https://raw.githubusercontent.com/Nesvilab/IonQuant/master/doc/Fig1.jpg" width="600"/>