Waters FUNC .IDX File Structure

This format stores information about UV and MS spectra.

These files are named something like _FUNC001.IDX.

Each FUNC .IDX file is paired by number with a FUNC .DAT file (which may be in the 2-byte, 6-byte, or 8-byte format). For example, _FUNC001.IDX is paired with _FUNC001.DAT.

FUNC .IDX files store the retention times as well as the number of data pairs recorded at each retention time. A data pair refers to a pair of mz-intensity or wavelength-absorbance values. The paired FUNC .DAT file stores the data pairs.

A FUNC .IDX file is comprised of contiguous 22-byte segments, one for each retention time. All known values in this file format are little-endian and unsigned. In order from start to end:

Data Type	Purpose
1 int	Offset of data in the paired FUNC .DAT
22 bits	Number of data pairs in the paired FUNC .DAT
10 bits + 4 bytes	UNKNOWN
1 float	Retention time (in min)
6 bytes	UNKNOWN

The entire file can be visualized by the following diagram. The segments are not drawn to scale.

+---------------------+--------------+---------+--------+---------+
| offset in FUNC .DAT | # data pairs | UNKNOWN | time 1 | UNKNOWN |
+---------------------+--------------+---------+--------+---------+
| offset in FUNC .DAT | # data pairs | UNKNOWN | time 2 | UNKNOWN |
+---------------------+--------------+---------+--------+---------+
| offset in FUNC .DAT | # data pairs | UNKNOWN | time 3 | UNKNOWN |
+---------------------+--------------+---------+--------+---------+
|              continues for every retention time                 |
+-----------------------------------------------------------------+

NOTE: FUNC .IDX files for Waters HRMS data have a different file structure. This is not documented because it is not yet understood.