Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Waters MassLynx

MassLynx is the data acquisition software for Waters mass spectrometers. There are several options available for processing Waters raw data into peak lists for searching with Mascot.

ProteinLynx Global Server is the Waters software environment for proteomics project management, protein quantification, and protein identification and characterization.

Mascot Distiller can process Waters raw data, both DDA and MS^E. Mascot Distiller can also be used as a data import filter by Mascot Daemon for batch processing of files. The advantage of using Distiller is that it provides comprehensive support for quantitation.

MSConvert is a free utility that can be used as a data import filter in Mascot Daemon 2.5.

ProteinLynx Global Server

PLGS supports Mascot Server, enabling workflows to be created to process Waters DDA or MS^E data into peak lists, submit the searches to Mascot, and import the search results back into PLGS. To configure Mascot as a database search engine in PLGS, from the options menu, choose preferences; search engines.


PLGS processing features include lockspray calibration and MaxEntLite, to create a singly charged, deisotoped peak list for searching. Expression Analysis provides a framework for relative quantitation experiments. Search results can be viewed and reported within the PLGS interface or you can open standard Mascot result reports via the Mascot search log.


Mascot Distiller

Mascot Distiller can be used to browse Waters raw data and process it into high quality peak lists that can be saved or submitted direct to a Mascot Server for searching. With the appropriate Distiller Toolboxes, the search results can be imported back into Distiller for further examination or used as the basis for quantitation. If the optional Mascot Daemon Toolbox is installed, these processes can be automated using Mascot Daemon.

Besides the quality of the peak lists, the other advantages of using Mascot Distiller are that it provides a universal interface to other raw file formats, and it is fully integrated with Mascot Server and Mascot Daemon. You can, for example, use Mascot Daemon to process batches of files automatically, saving Distiller project files that contain peak lists, search results, and quantitation results.


MSConvert is a component of ProteoWizard that converts between various file formats. It has a large number of options and can be configured as a data import filter in Mascot Daemon 2.5. Note that the input file format is not specified; msconvert auto-detects the format.



MassLynx and ProteinLynx Global Server are trademarks of Waters Corporation.