Mascot Distiller

Mascot Distiller, developed by Matrix Science, is a vendor-independent workstation application designed for quantifying proteins and peptides from Mascot database searches. It provides a single, intuitive interface to native ("raw") mass spectrometry data files from all major instrument manufacturers, including Agilent, Bruker, SCIEX, Shimadzu, Thermo, and Waters. It is suited to proteomics researchers, core laboratories, and industry users who require reliable, high-quality processing of raw MS data alongside trusted protein identification.

Beyond quantitation, Mascot Distiller offers a broad range of functionality for raw data processing, peptide identification, de novo sequencing, and batch automation. Multiple acquisition modes are supported, including MALDI MS and MS/MS (peptide mass fingerprinting), Data Dependent Acquisition (DDA) covering MS/MS, LC-MS/MS, and ddaPASEF, and Data Independent Acquisition (DIA) via Waters MSE, with Thermo and SCIEX DIA support coming soon.

Core Capabilities

• Native integration with Mascot Server for trusted and reliable protein identification by database searching
• Label-free quantitation (LFQ), including retention time alignment ("match between runs")
• Quantitation of peptides and proteins using any MS1 method with a precursor mass shift, including 18O, AQUA, ICAT, ICPL, metabolic labelling, and SILAC
• Interactive quantitation graphs and plots suitable for publication, with export to statistical packages
• Augmentation of database search results with de novo sequencing
• Improved peptide match quality through optimised peak detection

Supported File Formats

• Agilent MassHunter (Q-TOF)
• Bruker TDF (timsTOF, ddaPASEF) and baf (QTOF)
• SCIEX Analyst (5600, 6600, 7600 series)
• Thermo Xcalibur (LCQ, LTQ, Orbitrap)
• Waters MassLynx (QTof, M@ldi, TofSpec, Synapt) and MSE (DIA)
• mzML 1.1 and mzXML 2.0/2.1 XML interchange formats
• Additional data access libraries for older instruments and PMF experiments

Quantitation Workflow

• Quantitation is based on relative intensities of extracted ion chromatograms (XICs) for precursors in MS1 survey scans
• Compatible with label-free quantitation and any chemistry that creates a precursor mass shift (18O, AQUA, ICAT, ICPL, metabolic labelling, SILAC)
• Results can be visualised and exported as interactive graphs, HTML reports, and CSV spreadsheets
• Supports fractionated label-free quantitation and full reporting of quantitation datasets

Batch Automation with Mascot Daemon

• The Mascot Daemon Toolbox enables Mascot Distiller libraries to be called from Mascot Daemon for processing batches of data files
• Automatically submits searches to a Mascot Server and saves peak lists to disk
• Creates Distiller project files allowing raw data and peak lists to be opened directly via hyperlinks in Daemon
• Daemon saves database search results into the Distiller project file
• All stages of a quantitation experiment can be fully batch automated, from peak picking through to saving a complete quantitation report

Search Toolbox

• Display Mascot search results directly within Mascot Distiller
• Automatic de novo sequencing and automatic sequence tag calling
• Manual de novo sequencing and sequence tag tools
• Predict fragment ions from a peptide sequence and overlay them on an MS/MS spectrum
• Predict mass values from a protein digest and overlay them on a spectrum
• Top-ranking peptide matches for each peak list are displayed under a Mascot Search Results node in DataSet Explorer, labelled with peptide sequence and Mascot ions score

Optimised Peak Detection

• Unique peak picking algorithm that fits each peak to a complete isotope distribution
• Processes raw data from any instrument into high-quality, de-isotoped peak lists
• Detects peaks by fitting an ideal isotopic distribution to experimental data, adjusting mass, resolution, intensity, and charge state to maximise correlation
• Automatically determines charge state; peak lists contain only monoisotopic peaks even with poor signal-to-noise or unresolved isotopic distributions
• Smoothing is not necessary or required
• Peak lists can be viewed, sorted, edited, and saved to MGF format or a comprehensive format with additional per-peak information
• Peak lists can be submitted directly to a Mascot Server for database searching
• The entire workspace, including peak lists and preferences, can be saved to a project file

Licensing, Deployment, and System Requirements

• Available for 64-bit Microsoft Windows 7 SP1 or later, Server 2008 R2 SP1 or later, and fully compatible with Windows 11 and Server 2022
• Requires .NET Framework 4.6 or later; does not use a GPU — all computation is performed on the CPU
• Recommended hardware: Intel Core i9 or AMD Ryzen 9 processor with at least 16 cores, 32 GB RAM (64 GB preferred), and fast disk with at least 4 TB of space; NVMe is beneficial but not required
• Perpetual licence (not an annual fee), shipped as a digital download, typically installed on a workstation at the customer's own premises
• New licence includes one year of Premium Support: unlimited priority access to expert technical support, remote problem diagnosis, guided installation and migration, and free updates to any new release
• Support is provided directly by Mascot developers and experts based in the UK and USA
• After the first year, an optional annual support contract is available at 35% of the licence fee per year

Mascot Distiller integrates directly with Mascot Server for protein identification by database searching, and batch automation of quantitation workflows requires Mascot Daemon, which is shipped as part of Mascot Server. Matrix Science recommends using the latest release of Mascot Server for optimal compatibility.