• Supported formats of mass spectrometers producers
• Supported open formats
• AB/SCIEX
• Agilent Technologies
• Bruker Daltonics
• Wates / Micromass

click table to enlarge

The table above summarizes data formats, which can be easily imported into Spectrolyzer. Data formats where divided into two categories: formats of mass spectrometers producers and open formats, with publicly available specifications. If your MS manufacturer data cannot be read by the Spectrolyzer directly, in general, it can be always converted to one of the open formats, e.g. mzXML, mzML or mzData and then imported into Spectrolyzer.

Should you encounter a machine that does not seem to be compatible, please contact us and we will try come up with a way to import your data into Spectrolyzer.

According to the information provided in the table, please additionally note that:

• Thermo Xcalibur .raw files will be supported by the Spectrolyzer, provided that the MSFileReader or Xcalibur are installed on the same computer as the Spectrolyzer. 
• Waters/Micromass .raw directories are supported by the Spectrolyzer, using massWolf software, which is included in the distribution of the Spectrolyzer.

If one of your spectrometers format is not supported by the Spectrolyzer, there are freely available tools, which enable the conversion into one of the well-known XML-based formats, e.g. mzXML, mzML or mzData. All of these formats were developed to facilitate MS data analyses in an external software and are supported by the Spectrolyzer. The manufacturers of MS instruments often allow to save data in a text format, therefore we enable importing various data saved in a simple .txt or .csv.

There are different applications, which were developed to enable conversion between the MS manufacturers formats and open formats. Nevertheless, the large number of tools dedicated to the formats conversion often makes it difficult to find the one that would meet our needs. To facilitate importing data into the Spectrolyzer we provide the set of guidelines on how to convert various formats represented by the different producers of mass spectrometers. The instructions concern only conversion into open formats supported by the Spectrolyzer. By choosing one of the following producers of mass spectrometers you will be directed to its data conversion guidelines:

• AB/SCIEX
• Agilent Technologies
• Bruker Daltonics
• Waters/Micromass

The following AB/SCIEX data types can be manually converted to open formats:

• .wiff from Analyst software (QStar, QTrap instruments)
• .dat from Data Explorer (before 4.2) software (AB SCIEX Voyager (MALDI-TOF))

.wiff files conversion to mzXML or mzData 

There are two different ways to convert .wiff files to open formats:

1. Converting .wiff files to mzXML using mzWiff.

   mzWiff is a command-line program, which can be downloaded from the Sashimi project SourceForge, free of charge. mzWiff is also a part of the Trans-Proteomic Pipeline (TPP). Application requires the Analyst library from ABI/MDS Sciex to work properly, therefore the Analyst software has to be installed on a computer on which the conversion will be performed. Since the Analyst software is Windows platform dependent mzWiff works only under Windows. mzWiff replaces, improves and corrects mzStar software.
   
   

2. Converting .wiff files to mzXML or mzData using CCwiffer.

   CCWiffer stands for the "Charleston Core Wiff Converter". The software converts .wiff files to the xml based formats: mzXML or mzData. Application requires the Analyst library from ABI/MDS Sciex to work properly, therefore the Analyst software has to be installed on a computer on which the conversion will be performed. Since the Analyst software is Windows platform dependent CCwiffer works only under Windows. Software can be downloaded from its SourceForge. The user manual shows in details how the conversion should be performed.

.dat files conversion to .txt files

ASCII Spectrum and ASCII Chromatogram (.txt) data can be extracted from the .dat files using AB/SCIEX Data Explorer software. To convert an entire data file to an ASCII text file:

1. Open the data file you want to convert in Data Explorer.
2. From the File menu, select Convert, then select ASCII text. Save As dialog box is displayed.
3. Specify the name and destination for the file to be exported. By default, the software assigns a .txt extension to the file.
4. Click OK.

The more detailed information can be found in the Data Explorer 4.0 User Guide.

The following Agilent Technologies data types can be manually converted to open formats:

• .yep from DataAnalysis software (Agilent LC/MS Trap)
• .wiff from Analyst software (Agilent LC/MS TOF)
• .d directory from MassHunter software (Q-TOF)

.yep files conversion to mzXML

See how the .yep files conversion is performed with the Bruker software.

.wiff files conversion to mzXML or mzData

See how the .wiff files conversion is performed for the AB/SCIEX data types.

.d directory conversion to mzXML or mzML

There are two different ways to convert .d directories to open formats:

1. Converting .d directories to mzXML using trapper.

   trapper is a command-line program, which can be downloaded from the Sashimi project SourceForge, free of charge. trapper is also a part of the Trans-Proteomic Pipeline (TPP). Since the application uses MassHunter Data Accquisition Component (MHDAC), included within trapper by the Agilient permission, the installation of the MassHunter software is not required. The MassHunter libraries are Windows platform dependent, therefore trapper works only under Windows.
   
   

2. Converting .d directories to mzXML or mzML using msconvert.

   msconvert is a command-line program, converting between various file formats, included in the ProteoWizard tools and libraries. msconvert can be used in the following way:
   > msconvert data.d
   (creates data.mzML in current directory)
   > msconvert data.d --mzXML
   (creates data.mzXML in current directory)
   Other examples showing how to use msconvert can be found in the ProteoWizard documentation.

The following Bruker data types can be manually converted to mzXML:

• .baf from flexAnalysis software (APEX, micrOTOF, micrOTOF-Q instruments)
• .yep from flexAnalysissoftware (Esquire instrument family)
• AutoXecute run for LC-MALDI (autoFlex, ultraFlex instrument family)
• .fid from XMASS/XTOF software (Flex instrument family)

.baf, .yep, .fid and AutoXecute conversion to mzXML

All these data types can be converted to mzXML using Bruker software: CompassXport. The software can be downloaded free of charge from the Bruker's site. The detailed instructions how to download and install the CompassXport, and also how to perform data conversion are available here.

The following Waters/Micromass data types can be manually converted to open formats:

• .pkl files from MassLynx software (all Waters/Micromass mass spectrometers)

.pkl conversion to mzXML

There are two different ways to convert .pkl files to open formats:

1. Converting pkl files to mzXML using pkl2mzXML.

   pkl2mzXML is a command-line program, which can be downloaded from the Sashimi project SourceForge, free of charge. pkl2mzXML is also a part of the Trans-Proteomic Pipeline (TPP).
   
   

2. Converting pkl files to mzXML using ProteomeCommons.org IO Framework.

   ProteomeCommons.org IO Framework is Java based, free and open-source application for handling different spectra and peak lists files. Its main functionality is to read and write mass spectra of various formats. The software can be downloaded from its webpage. Since it uses Java Web Start and requires Java 5 or greater to run, it is platform independent. ProteomeCommons.org IO Framework supports reading and writing of the .pkl and mzXML formats, therefore it is possible to read data from a .pkl file and save it as a mzXML easily. You can find the detailed information about the software and its capabilities here.