converting Shimadzu MSMS chromatograms

[oktanol]

Hi there,
We would really like to convert MRM chromatograms from Shimadzu's LabSolution file format to something that could perhaps be converted to MassLynx files (that is .lcd or maybe .jdx to .raw). Is there any way of doing this? Via .cdf doesn't seem to work because it only saves the parent ion, so the signal is o.k. but if two fragment ions are monitored then you can't really distinguish between them (or at least the quantification method can't). Also it creates lots of files for every run. Or is there perhaps a way of compiling it?
I'm dreading the thought of having to use this awkward way of correcting the automatic integration if I don't like what it has done - who came up with this silly idea of separately changing the baseline in a horizontal and vertical way while you can't even see where you drop it??? And with the licence they have for the software I can only do it in the lab and nobody else can do it there, so that's why I'm quite keen to convert the files somehow.

Many thanks for any help!
Claudia

[lmh]

I can't help in converting Shimadzu files to MassLynx, but you should be able to see what the Shimadzu integrator is doing with base-lines... it should display them quite clearly. The software is fairly complex but also fairly versatile and powerful. If you've only got one licenced copy so you're having to do everything on the instrument PC, it's likely you aren't getting adequate time to learn how to use the software properly. It has some bits that I find unnecessarily complicated, like distinguishing (in MS, not in PDA) between integration for qualitative purposes (displayed in the main chromatogram area) and integration for quantitative purposes (which has a different set of integrator settings, and is displayed on the compounds tab of the results view, which a lot of people don't even know exists because someone will have dragged it to an invisibly small window at the bottom of the screen...)
I'd suggest revisiting the Shimadzu software, and also, seriously, hassle whoever owns the lab into getting at least one process-only licence for the software.

Here's a mini-rant on software: Several major manufacturers have scant protection on their software. I don't know if this is deliberate. It means they can sell to academic organisations with little cash, because although the organisations can't afford the licences they need, and the big-important-people who set policy for the companies won't negotiate licence arrangements that work, the sales and engineer staff who actually interact with customers can quietly suggest they install multiple copies and ignore the licencing. This completely fouls up those organisations who sit in the middle, academic, public-funded, not rolling in cash, but who feel obliged to stick to the right side of the law. We have to pay a fortune for licences that we know similar organisations simply ignore, which decreases our competitiveness in attracting funding. Shimadzu are one of the few companies who've made the process fair, and levelled the playing-field, by using a USB key. It's irritating, but that's how it is. You definitely need another licence for a stand-alone data-handling PC somewhere. Otherwise you will never get the best from the instrument (and why waste a large expensive instrument for the sake of its much cheaper licence?).

[oktanol]

Hmm, perhaps I'm doing it totally wrong then? Will need to check this. So far it seems to me as if for changing the automatic integration (which works better than what I was used to from other programs but sometimes you will still need to correct it) you have to separately changed the baseline in a horizontal and vertical way. For both ways the mouse arrow turns into a vertical line which is fine for horizontal but isn't working at all for vertical because you can't see where you are going to click. I can see the baseline itself once I've placed it somewhere (wrong) but not where I'm going to drop it while being in the process of changing it vertically.

Wondering if anyone else is familiar this?

What I want to do is pick one end of the baseline and place it wherever I like, then the other end, do the same, ready, intuitive, and a pretty old way of doing it... Not clicking lots of buttons and trying at least 5 times to get it in the right place. Seems almost unbelievable that this isn't possible.

[lmh]

I think what you're doing is manual integration. I am not particularly experienced at this, as personally I prefer to use the automatic integrator to find my peaks, and tend to spend some time trying to find integrator settings that give acceptable integration of all of my samples, rather than reviewing samples individually and moving baselines as necessary.

Have you worked out Shimadzu's philosophy for manual integration? I believe it to be this:

(1) Baselines are initially assumed to start on the curve rather than somewhere below it. For this reason, the first tool, "Move BL" allows you to move the start and end of a peak sideways, and the vertical position of the start or end is always exactly on the chromatogram's data at the time-point you selected.

(2) Nevertheless, it's understood that the signal may be above baseline at the time where you want to start the peak. If so, Shimadzu assume you will want to start the peak at a vertical level that corresponds to a real baseline measurement. They assume you will select a piece of genuine baseline somewhere else in the chromatogram, and use the vertical level (the signal) at this time-point. This is what the second tool, "Move BL vertical" actually does. It allows you to select a time-point (horizontal position!!) at which you believe the vertical position to be genuine baseline (this is why it shows you a vertical-line cursor - because you are selecting a time on the x-axis, not a vertical position). It then leaves the peak baseline starting at the original retention time, but moves it vertically to the place where the chromatogram intersects the vertical cursor line, at the time you selected as your baseline-point.

So far as I know, Shimadzu haven't provided a tool giving a free drag-and-drop to move the baseline to wherever you feel is appropriate. I think they're very measurement-based and don't provide things that don't use the measured data in some direct way.

The remainder of their tools have similar constraints; each tool targets some particular issue that might have happened in typical chromatography, and allows you to make some decision about how to respond (drop-lines or valleys etc.), but it's never a free choice, always one that differentiates between known solutions to known scenarios.

[oktanol]

Yep, that's how it seems to work, very awkward.
I do use automatic integration, but sometimes I'm not happy with what it did...