Vendor Formats

OpenMS reads two vendor formats directly, without a conversion to mzML first: Thermo Fisher .raw files and Bruker timsTOF .d directories. The OpenMS installers and the pyOpenMS wheels include both readers. For all other vendor formats, convert the data to mzML first, for example with ProteoWizard’s msconvert.

Thermo Fisher .raw

OpenMS reads .raw files with Thermo’s RawFileReader library, which runs on .NET. It needs the .NET 8 runtime (or newer). How to install it, and how to point OpenMS to a runtime in a non-standard location with DOTNET_ROOT, is described in Reading Thermo Fisher RAW files on the installation page for Linux, macOS and Windows.

RawFileReader reading tool. Copyright © 2016 by Thermo Fisher Scientific, Inc. All rights reserved.

Converting with FileConverter

FileConverter converts .raw files with one of two readers, chosen with -RawToMzML:reader:

inprocess

external

Default on

Linux and macOS

Windows

Reader

built into OpenMS

ThermoRawFileParser, run as a separate program

Needs

.NET 8

on Windows the .NET Framework that Windows includes; on Linux and macOS mono, which the OpenMS packages do not include

Output

every format FileConverter writes

mzML only

The Windows installer puts ThermoRawFileParser on the PATH, so the external reader works there without further setup. Elsewhere, give its location with -RawToMzML:ThermoRaw_executable and the mono executable with -RawToMzML:NET_executable.

Both readers apply Thermo’s peak picking by default, so the output holds centroided spectra. -RawToMzML:no_peak_picking keeps the spectra as they were acquired, and -RawToMzML:include_noise adds the noise data.

FileConverter -in sample.raw -out sample.mzML

Reading .raw in other tools

These tools also accept .raw files as input: CometAdapter, FeatureFinderCentroided, FeatureFinderIdentification, FeatureFinderLFQ, FeatureFinderMetabo, FeatureFinderMetaboIdent, FeatureFinderMultiplex, FLASHDeconv, IsobaricAnalyzer, MassTraceExtractor, MetaboliteSpectralMatcher, MS1LabeledWorkflow, NucleicAcidSearchEngine, OpenPepXL, OpenSwathPeakMapExtractor, OpenSwathWorkflow, ProSE, ProteomicsLFQ, SageAdapter and SimpleSearchEngine.

They read with the built-in reader, on every platform, so they need the .NET 8 runtime on Windows as well. Like FileConverter, they apply Thermo’s peak picking, so they process centroided spectra. To process the spectra as they were acquired, which for most Orbitrap methods means profile MS1 spectra, convert the .raw file with FileConverter -RawToMzML:no_peak_picking first and use the mzML.

Note

OpenNuXL also accepts .raw files. It converts them with ThermoRawFileParser, like the external reader of FileConverter, so on Linux and macOS it needs mono.

Bruker timsTOF .d

OpenMS reads the .d directories of timsTOF instruments (TDF format, with an analysis.tdf file) with the opentims library. A .d directory packed into a ZIP archive (.d.zip) can be given instead; it is unpacked into a temporary directory while the tool runs, so that directory needs space for the unpacked data.

Bruker’s SDK is not needed: OpenMS computes m/z and ion mobility (1/K0) from the calibration stored in the file. If Bruker’s SDK library (timsdata.dll or libtimsdata.so) is installed, set the environment variable OPENMS_BRUKER_SDK_PATH to the library’s path to convert ion mobility with Bruker’s own code instead.

These tools accept .d and .d.zip input: CometAdapter, FeatureFinderIdentification, FeatureFinderLFQ, FeatureFinderMetaboIdent, FileConverter, IonMobilityBinning, MetaboliteSpectralMatcher, NucleicAcidSearchEngine, OpenSwathPeakMapExtractor, OpenSwathWorkflow, PeakPickerIM, ProSE, ProteomicsLFQ, SageAdapter, SimpleSearchEngine and TransitionListEvidenceFilter.

The acquisition type is detected from the file:

  • DDA-PASEF: one MS1 spectrum per frame, which stores the ion mobility of every peak, and one MS2 spectrum per precursor with a single ion mobility value.

  • DIA-PASEF: MS1 as above, and one MS2 spectrum per frame and isolation window, which stores the ion mobility of every peak.

FileConverter, CometAdapter and PeakPickerIM have bruker: options to change this, for example -bruker:export_mode to force the per-precursor layout (spectrum) or raw frames (frame). FileConverter can also skip the MS1 spectra (-bruker:load_ms1 false), recalibrate m/z, aggregate neighbouring frames and centroid along the ion mobility axis; see its documentation. ProteomicsLFQ centroids the MS1 frames along the ion mobility axis before feature detection. The other tools read with the default settings.

To convert a .d directory to mzML:

FileConverter -in sample.d -out sample.mzML

pyOpenMS

pyOpenMS reads both formats as well; see Vendor formats in the pyOpenMS user guide.