We are using different MS Equipment (Bruker - MALDI, Thermo - Orbitrap...).
I generally analyse my data using Thermis Xcalibur. I now recorded Spectra on the MALDI and exported them as .mzML. The converter tool in Xcalibur does not accept this format and most converters only convert .raw to .mzML and not the other way around. Does anyone have suggestions? Thank you in advance.
The MS Manufacturer's generally only export to mzXML and other open formats. They provided public .dll's for this purpose that will read their proprietary file formats and allow you to convert to other "open" formats. MSConvert is an open source package to do that. Unfortunately, they want to keep their data formats proprietary for some stupid reason, so they won't release converters to go the other way. I think it is to lock customers into their ecosystems. I would recommend trying to go to one of the open source LC/MS/MS packages for your analysis (e.g., MZmine or OpenMS) this gives you more control over your analyses from multiple sources.. It is possible to get individual scans back through an ASCII scan import feature that is available from most vendors, but you will find that most of the manufacturers have tweaked their analysis software to use metadate from their files and it won't work well on other vendor's data, particularly cross MS platform types (e.g., Iontrap to TOF to Orbitrap). See the link below for a primer.
Method Mass Spectral Data Processing
Hello.
Take a look at this page (http://www.ms-utils.org), but I'm not sure that the Xcalibur software is compatible with the Bruker MALDI spectra. Otherwise the flex Analysis is a very sophisticated data analysis tool.:-)
Thank you all for your answers! I now went with a freeware programm to analyze these spectra generally and went back to Flex Analysis for more detailed analysis.
Lev, FlexAnalysis is Bruker software.
https://bruker-daltonics-flexanalysis.software.informer.com/3.3/
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