Isn't it time for an open source chromatographic format [Bioanalytics]

posted by ElMaestro  – Denmark, 2018-11-04 21:54  – Posting: # 19527
Views: 1,784

Hi all,



I think it would be great if an open source format for time series of chromatograms data were defined (i.e. something as simple as signal (counts per second etc) as function of time) and if the big software vendors would allow import of such files for quantification with the proprietary peak finding and integration algos in Analyst, MassHunter, MassLynx etc.

There is simply no reason not to do this apart from IP and it would make enormously good sense from a QA perspective. Might also increase competition about companies developing serious algos. Comparing areas of identical appearance between packages is one thing (and currently impossible!), but comparison of absent peaks or S:N < 5 etc would also be facilitated as would bias/behaviour in case of tailing and much more. As of present there is not even a definition of how to quantify S:N (how would you do it? Is your way better than mine? No? In which implementation context does a regulatory requirement about it make sense).

One of the packages happily assigns an RT to a split peak or identifies "a peak on a peak" (and is able to subtract areas accordingly) while other packages don't seem do that. Depending on circumstances this may be desirable or not. I was recently at a CRO were the SOP said that a split peak is defined as one a cluster of CPS offset from baseline assigned two RTs. With the introduction of a station from another vendor and thus other software that SOP actually seemed to become partially irrelevcant for the new station. And so forth. I am using the term 'seemed' here because the behaviour is not defined in manuals and the software vendor is completely silent when asked. No can talk, much secret, highly intellectual property, hush hush.

We need an open source format for chromatographic data. It could be as simple as two columns in a CSV-file plus some meta data.

We need it. Full stop.

if (3) 4

x=c("Foo", "Bar")
b=data.frame(x)
typeof(b[,1]) ##aha, integer?
b[,1]+1 ##then let me add 1



Best regards,
ElMaestro

"(...) targeted cancer therapies will benefit fewer than 2 percent of the cancer patients they’re aimed at. That reality is often lost on consumers, who are being fed a steady diet of winning anecdotes about miracle cures." New York Times (ed.), June 9, 2018.

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