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Shimadzu Scientific Instruments

Shimadzu Scientific Instruments offer two instrument lines suitable for proteomics. The current MALDI instrument line can generate PMF and MS/MS data from peptides and proteins:

  • AXIMA Series (PMF, MS/MS)
  • MALDI-80X0 (PMF, ISD)
  • MALDImini (PMF, MS/MS)

The LCMS QTOF line of instruments can be used for DDA and DIA proteomics:

  • LCMS-9030
  • LCMS-9050

There are a two file formats: .run files from the AXIMA Series of MALDI instruments and .lcd files from the LCMS QTOFs. The data can also be exported from the Shimadzu software and saved as mzML files.

Mascot Distiller

Mascot Distiller can be used to browse Shimadzu raw data files. Distiller can also open and browse the mzML files. Distiller processes them into high quality peak lists that can be saved or submitted directly 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.

Shimadzu .run or .run.gz format

Mascot Distiller supports processing .run files, which can also be compressed as .run.gz files. To open these files, Mascot Distiller requires the gzip.exe program, supplied with Launchpad, to be on the system path. A complete LC MALDI run can also be opened and processed by Distiller.

Shimadzu .lcd format

This is the native file format for the LCMS QTOF instruments. Mascot Distiller requires the Shimadzu LCMS-IT-TOF Data Export Library (TTFLDataExport) 1.02 to be installed on the PC in order to open them.

mzML

mzML files are an open XML standard for mass spectrometer data developed by the Proteomics Standards Initiative (PSI) of the Human Proteome Organisation (HUPO). Shimadzu software can export raw data into the mzML format that can then be opened and processed by Mascot Distiller. This includes both DDA and DIA data from LCMS QTOFs.

Mascot Daemon

Mascot Daemon can be used to process batches of raw files by choosing Mascot Distiller as the data import filter.

Mascot Distiller requires the optional Mascot Daemon Toolbox to allow the Distiller libraries to be called from Mascot Daemon. When this toolbox is active, Mascot Distiller will appear automatically on the list of data import filters in Daemon.

Shimadzu .lcd files and .mzML files are straightforward to process through Mascot Daemon once appropriate data import filter has been selected.

Shimadzu MALDI Solutions Data Acquisition

The MALDI Solutions Data Acquisition application integrates directly with the public or in-house Mascot Server. There is a walkthrough that covers data acquisition and searching with Mascot Server produced by Shimadzu, available on YouTube.

ProteoWizard msConvert

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. msConvert supports both .lcd and mzML file formats.