wiff format

[wangjiawen2013]

Hi,

Can mhcquant support wiff format internally, or we must convert to mzML first ?

The raw data generated by the AB 6600 (SCIEX TripleTOF 6600) are in .wiff + .wiff.scan format (and sometimes accompanied by .analysis files). These are proprietary raw mass spectrometry data formats from SCIEX.

✅ Brief explanation

Instrument: SCIEX TripleTOF series (e.g. 5600 / 6600 / 6600+)

Raw output file formats:

xxx.wiff
The main file containing metadata, acquisition methods, and partial data

xxx.wiff.scan
Stores the complete spectral (scan) data

Optional accompanying files:

xxx.wiff.mtd – method-related metadata

xxx.wiff.analysis – processing and analysis information

👉 The .wiff and .wiff.scan files must be used together in order to correctly read the raw mass spectrometry data.

[jonasscheid]

Thanks for the issue @wangjiawen2013! I think it would be great if mhcquant would support .wiff natively. @timosachsenberg OpenMS currently does not offer this conversion, right? So users need to use msconvert beforehand I guess and then use the mzML as input, correct?

[jonasscheid]

Looks like this is not the case @wangjiawen2013. Could you try converting to mzML via msconvert and report back if it works or you ran into any errors?

[wangjiawen2013]

Ok, I'll try.