Waters MassLynx stores every run as a .raw folder: one _FUNCnnn.DAT file per scan function
(MS scans, SIR or MRM channels, PDA spectra) with its .IDX scan index, _CHROnnn.DAT files for
analog channels such as a UV, ELSD or pressure trace, and _HEADER.TXT with the sample details.
None of it opens without MassLynx. This page reads the folder directly.
How to convert a .raw folder
- Pack the folder: on Windows right-click it and choose Send to, Compressed (zipped) folder; on a
Mac choose Compress. A ZIP with several
.rawfolders converts them all. You can also select the files inside one folder and upload them together. - Choose the number format and, for PDA data, the wavelengths you want as chromatograms.
- Download the CSV files or the Excel workbook.
What you get
- SIR and MRM data (triple quadrupole and single quadrupole methods): one CSV per function with a
column per channel, named like
Function 1 MRM 112.97 > 40.00 (ES+). - MS scans (quadrupole and Q-TOF): the total ion chromatogram with the base peak of every scan, and a table of every m/z value and intensity. Q-TOF masses are corrected with the run's root-mass calibration where it has one.
- PDA spectra as a time × wavelength table in mAU, with chromatograms extracted at chosen wavelengths.
- Analog channels with the names and units the run gives them: UV and ELSD traces, system pressure, solvent composition.
- Run details: sample name and description, vial, instrument, MS, inlet and tune methods, acquisition date.
How the numbers were checked
MassLynx writes the total ion current of every scan into the scan index while it acquires. Every function we decode is checked against those totals, and a function that does not add up is exported as the stored total only, with a warning, never as guessed numbers. On all 13 test runs (among them a Xevo TQ-XS, a ZQ, an older Q-TOF and seven Q-TOF runs from a public data set) every function adds up. The older Q-TOF run also matches the values ProteoWizard reads with the Waters library, and the PDA and analog values match the open-source reader rainbow.
Not supported yet
- Folders from SYNAPT and Xevo G2 class instruments (a 30-byte scan index, often with ion mobility data) are recognised and refused with an explanation.
- Thermo
.rawfiles share the extension but are a different format; they are refused too.
More about what this tool reads and writes: Chromatography Data Converter (Agilent, Shimadzu, Waters, AIA).