Comment on a PREreview of "Seeking community input for: mzPeak - a modern, scalable, and interoperable mass spectrometry data format for the future"

This Zenodo record is a permanently preserved version of a comment on a PREreview. You can view the complete PREreview and comments at https://prereview.org/reviews/14933345. Thanks to the authors for coming up with this suggestion. I appreciate the effort to harmonize the data storage across instrument vendors in a compressed format. I have some thoughts on the topic that may be useful to think about: I am wondering if you already have confirmed support from the instrument vendors? I think what makes proprietary formats good for them is that they can change and adapt them easily, if they introduce a new technique, analyser, and so on. In an open format that is controlled by CVparams like mzml, a new technique may lead to new vocabulary being introduced. This would be way ahead of market release of the new instrument and thus potentially give away their innovation to others. If i was a vendor, i would be reluctant of that. I agree with Yasin's comment that having metadata as free text would not be beneficial. I know that the preprint did not make any specific statement in what way the metadata would be included, but it should be noted that an undefined text provides no real benefit, because everybody would define, write, and parse it differently. (E.g. the 'comments' field in msp libraries or any community generated msp/mgf file) Spectra and chromatograms from other detectors should be included in the mzPeak data (as stated by the authors). In addition, it might be useful to optionally add additional traces (e.g. pump pressures, charge aerosol detector, ELSD, …) from external files, such as .csv files. In that case, the comment of non-matching instrument setups (e.g. non-Thermo LC with Orbitrap) may be adressed. Anyway, I am looking forward to any future news on this topic and thank you for the effort! Best Steffen Competing interests The author of this comment declares that they have no competing interests.