Mascot Distiller
Mascot Distiller Workstation offers a single, intuitive interface to a wide range of native (binary)
mass spectrometry data files. A unique algorithm, which fits each
peak to a calculated isotope distribution, processes the raw data into
high quality, de-isotoped peak lists.
This core functionality can be extended by adding one or more toolboxes. These are optional
collections of tools for specific tasks, such as Mascot search
result review, automatic and manual de novo sequencing, and batch processing.
There is also a developer's
package that provides access to the API of the underlying COM library.
How it Works
Mascot Distiller detects peaks by attempting to fit an ideal isotopic distribution
to the experimental data. This ideal distribution is predicted from the elemental
composition expected for a peptide of average amino acid composition at that point
on the mass scale. The profile of the ideal distribution is then adjusted by varying
the mass, resolution, intensity, and charge state, so as to maximise the correlation
with the experimental data. Once the best fit has been obtained, the peak is added
to the peak list and the corresponding signal subtracted from the spectrum. The process
is repeated until all the significant peaks have been fitted.
Similar approaches have been described by
- Berndt, P., et. al., Reliable automatic protein identification
from matrix-assisted laser desorption/ionization mass spectrometric
peptide fingerprints,
Electrophoresis (1999), 20, 3521-6, and
- Gras, R., et.al., Improving protein identification from peptide mass
fingerprinting through a parameterized multi-level scoring algorithm
and an optimized peak detection,
Electrophoresis (1999), 20, 3535-50.
The advantage of this approach over conventional peak detection is that the complete
experimental isotopic distribution is fitted, not just the 12C peak. The charge state
is automatically determined and the peak list contains only monoisotopic peaks, even
when the signal to noise is poor or the isotopic distribution not fully resolved.
Smoothing is not necessary or desirable.
Cross-platform data browser
Mascot Distiller supports all the following data file formats:
- Agilent
 DataAnalysis (yep) (LC/MS Trap)- Analyst (wiff) (LC/MS TOF)*
- MassHunter (Q-TOF)
- Applied Biosystems
 Analyst (QStar, QTrap) Data Explorer (Voyager*, 4700, 4800)
- Bruker
 Data/Flex Analysis (yep) format (Esquire)- Data/Flex Analysis (baf) format (Apex, MicrOTOF)
- XMASS/XTOF (Reflex, Biflex, etc.)
- Shimadzu
 Kompact (Axima) LCMSSolution (LCMS-IT-TOF)*
- Thermo
 Xcalibur (LCQ, LTQ, Orbitrap)
- Waters
 MassLynx (QTof, M@ldi, TofSpec)
- mzXML 2.0 and 2.1 (XML interchange format)
- Text (ASCII mass and intensity values)
* For these formats, Mascot Distiller requires access to library files (DLL's or OCX's)
supplied as part of the corresponding instrument data system.
Optimised Peak Detection
The main problems with conventional peak-picking algorithms are:
- Failure to pick low intensity peaks
- Picking peaks that are just noise
- Selection of the wrong peak(s) or all peaks in an isotopic cluster
- Need to continually "tweak" parameters
The algorithm used in Mascot Distiller addresses all of these problems by fitting the
complete isotope distribution, then applying two thresholds to the peak list - signal/noise
ratio and correlation coefficient. The result is peak detection, not noise detection:
Peak lists can be viewed, sorted, edited and saved to MGF and DTA format files, as well as a
comprehensive format that includes additional information for each peak. Peak lists can
be submitted direct to a Mascot server for database searching.
The entire Mascot Distiller workspace, including peak lists and preferences, can be saved to
a project file.
Daemon Toolbox
The Mascot Daemon Toolbox
enables the Mascot Distiller libraries to be called from Mascot Daemon,
to process batches of data files and submit searches to a Mascot server.
Peak lists are saved to disk automatically, and Distiller project files can also be created,
allowing the raw data and peak list(s) to be opened in Distiller by
clicking on a hyperlink in Daemon.
(Note: Mascot Daemon is a component of the Mascot Server package)
The Search Toolbox
is a collection of tools for protein identification and characterisation:
- Display Mascot Search results within Mascot Distiller
- Automatic de novo sequencing
- Automatic sequence tag calling
- Manual de novo and sequence tag
- 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
In the case of an MS/MS search, the top ranking peptide matches for each peak
list are displayed under a Mascot Search Results node in DataSet Explorer.
Each match is labelled with the peptide sequence and Mascot peptide score.
The Search Toolbox includes a powerful de novo sequencing algorithm:
Implements quantitation based on the relative intensities of extracted ion chromatograms for precursors
in survey scans. This approach can be used with any chemistry
that creates a precursor mass shift, for example, 18O, AQUA, ICAT, ICPL, Metabolic labelling,
and SILAC. However, please note that "label-free" is not yet supported.
Individual ratios are automatically accepted or rejected by means of user defined quality thresholds.
Corrections for isotope impurity and overlapping distributions are built in and overlays
show how well the experimental peaks fit to the ideal dsitributions. The quantitation results can be exported as
XML or transformed into HTML reports by XSLT style sheets.
Developer Toolbox
The Developer Toolbox contains the documentation and support to develop and run programs
that call the Mascot Distiller libraries. Distiller uses COM, so can be called from most
Microsoft Windows programming languages. The Developer Toolbox provides a uniform
Application Programmer Interface to all of the different raw file formats, greatly
reducing development time.
A run-time licence is required to execute the programs you develop on a PC
which does not have Mascot Distiller Workstation installed.
System Requirements
Mascot Distiller requires Microsoft Windows 2000, XP Professional,
Server 2003, Vista, or Server 2008. To submit a Mascot search
directly from Mascot Distiller Workstation requires Microsoft Internet Explorer 5.5 or later.
The Mascot server must be 2.0 or later, except for the Quantitation Toolbox, which requires Mascot server 2.2 or later.
For a few data file formats, Mascot Distiller makes use of
library files (DLL's or OCX's) that are supplied as part of the corresponding
instrument data system. These formats are marked with an asterisk in the list above.
Evaluation
If you wish to evaluate Mascot Distiller, you can obtain a 30 day trial licence by sending
an email request to support@matrixscience.com.
The software can be downloaded from the Distiller Support page.
Note that Mascot Distiller will not function without a valid licence.
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