Isn't it time for an open source chromatographic format [Bioanalytics]
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.
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.
—
Pass or fail!
ElMaestro
Pass or fail!
ElMaestro
Complete thread:
- Isn't it time for an open source chromatographic formatElMaestro 2018-11-04 21:54
- Isn't it time for an open source chromatographic format nobody 2018-11-05 09:00
- and now that we are at it ElMaestro 2018-11-05 13:53
- and now that we are at it nobody 2018-11-05 16:33
- and now that we are at it ElMaestro 2018-11-05 18:19
- Transparent ruler – like in the good ol’ days Helmut 2018-11-05 20:39
- Transparent ruler – like in the good ol’ days Ohlbe 2018-11-05 22:14
- Transparent ruler – like in the good ol’ days ElMaestro 2018-11-05 22:43
- Slow down, you move too fast […] Feelin’ Groovy Helmut 2018-11-06 02:05
- Slow down, you move too fast […] Feelin’ Groovy nobody 2018-11-06 09:29
- Yes it went a little fast ElMaestro 2018-11-06 11:09
- Yes it went a little fast nobody 2018-11-06 12:05
- Yes it went a little fast ElMaestro 2018-11-06 12:10
- Yes it went a little fast Helmut 2018-11-07 16:09
- Yes it went a little fast ElMaestro 2018-11-07 16:22
- Yes it went a little fast nobody 2018-11-07 18:30
- Purpose of S:N? Helmut 2018-11-08 09:46
- Purpose of S:N? ElMaestro 2018-11-08 22:27
- Purpose of S:N? nobody 2018-11-09 10:06
- Purpose of S:N? Helmut 2018-11-09 11:34
- Purpose of S:N? nobody 2018-11-09 12:08
- Purpose of S:N? Helmut 2018-11-09 12:34
- Purpose of S:N? nobody 2018-11-09 12:08
- Purpose of S:N? Helmut 2018-11-09 11:34
- Purpose of S:N? Helmut 2018-11-09 11:26
- Purpose of S:N? ElMaestro 2018-11-09 13:16
- Purpose of S:N? nobody 2018-11-09 10:06
- Purpose of S:N? ElMaestro 2018-11-08 22:27
- Yes it went a little fast ElMaestro 2018-11-07 16:22
- Yes it went a little fast Helmut 2018-11-07 16:09
- Yes it went a little fast ElMaestro 2018-11-06 12:10
- Yes it went a little fast nobody 2018-11-06 12:05
- Yes it went a little fast ElMaestro 2018-11-06 11:09
- Slow down, you move too fast […] Feelin’ Groovy nobody 2018-11-06 09:29
- Slow down, you move too fast […] Feelin’ Groovy Helmut 2018-11-06 02:05
- Transparent ruler – like in the good ol’ days ElMaestro 2018-11-05 22:43
- Transparent ruler – like in the good ol’ days Ohlbe 2018-11-05 22:14
- and now that we are at it nobody 2018-11-05 16:33
- and now that we are at it ElMaestro 2018-11-05 13:53
- Isn't it time for an open source chromatographic format paulhurleyuk 2018-11-05 16:27
- Isn't it time for an open source chromatographic format nobody 2018-11-05 09:00