What file formats, data types and instrument types are supported?

File formats

Progenesis LC-MS directly supports many of the most common data formats produced by LC-MS machines. It also offers an extension mechanism by which new formats can be supported (see the custom development section below).

The following list gives the various file formats currently supported, both those that are pre-packaged with the software and others that can be downloaded to extend your existing software:

• mzXml
• mzML
• Waters (MassLynx) .RAW folders (with dead time correction)
• Thermo (Xcalibur) .RAW files
• Agilent (MassHunter) .d folders
• Bruker Daltonics .d folders
• NetCdf .cdf files

Currently, other formats should be converted to mzML or mzXml. For example:

• ABSciex wiff files may be converted using msconvert.exe from ProteoWizard.

Custom development

We're happy to work with you to develop custom add-ons that support other file formats you may prefer to use. If you're interested in this option, please email support@nonlinear.com and one of our development team will contact you to discuss your needs and how we might help.

Data type

Data may be in either Profile or Centroided forms although you will usually get the best results using profile data. Additionally, if you use centroided data you will be asked to enter the full width at half maximum (FWHM) resolution of the machine on which the data was collected.

Instrument types

Progenesis LC-MS works with a wide variety of machine types. For most instrument types the default peptide detection method in Progenesis LC-MS should be used. For low resolution ion trap instruments, the specialised low resolution detection method option in Progenesis LC-MS should be used. We have also included an option for optimum detection of runs from Thermo FT-ICR instruments, which typically has much lower levels of noise than data from other instrument types.