Waters instruments

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.

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.

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

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

Mascot Distiller (DDA, MS^E)

Mascot Distiller can process and visualise Waters raw data acquired in DDA and MS^E modes. Spectra are processed into high quality peak lists that can be saved or submitted direct to a Mascot Server for searching. The search results can be imported back into Distiller for further examination or used as the basis for quantitation. These processes can be automated using Mascot Daemon.

Besides the quality of the peak lists, Mascot Distiller 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.

See also Automated processing with Mascot Daemon real-time monitor.

ProteinLynx Global Server (DDA, MS^E)

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.

MSConvert (DDA)

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. Note that the input file format is not specified; msconvert auto-detects the format.

Acknowledgements

MassLynx and ProteinLynx Global Server are trademarks of Waters Corporation.