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Agilent instruments

Agilent instruments are divided into multiple families, but the main instrument family used for DDA proteomics is the Quadrupole Time of Flight LC/HRMS (e.g. Revident, 6546, 6545XT, 6530). There are also several legacy models, such as 6300 series Ion Traps, older 6500 series Q-TOFs and 6400 series Triple Quads.

Agilent instruments use one primary data format: .d MassHunter format

Mascot Distiller (DDA)

Mascot Distiller can process and visualise Agilent raw files. Distiller processes them 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 steps can be automated using Mascot Daemon.

Agilent .d format

Mascot Distiller supports processing .d files containing DDA spectra. The Agilent .d format is a folder rather than a file. When opening the format in Distiller, select the .d folder and Distiller will go ahead and open the data.

Agilent .d MassHunter folders are straightforward to process through Mascot Daemon. Use the “Add Folder” button and select the .d MassHunter folder. The button will be inactive until you have set up an appropriate data import filter.

Agilent MassHunter (DDA)

Agilent MassHunter Qualitative Analysis can process DDA data and generate MGF files ready for searching via the Mascot Server web interface or as a batch with Mascot Daemon. Agilent have published an application note that recommends MassHunter Qualitative Analysis settings for the data extraction and has a walk through for processing data and searching the MGF peak lists using the public Mascot Server or your own locally licensed server.

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.