Is it possible to open an ICP-MS laser file, in this case a series of spots for different elements, and have iolite fit the baseline and find the peaks without an associated laser log file?
Basic processing of data without a laser log
bpjackso
It can be done semi-automatically if the instrument in question supports sample labels and they've been configured. If the data are a continuous stream without any metadata to determine the sample starting and ending times, it would need to be done manually.
Depending on how many files need processing and how long it takes to do manually, it would also be possible to invest some time in developing a python script to automate it without using the built-in tools.
If you want more specific advice, you can share an example data file with the iolite support email.
All the best,
- Joe
Just in addition to Joe's points: it can be done 'semi-automatically' using a beam intensity approach. You can select baselines where a certain channel's beam intensity is less than a defined amount, and you can similarly select 'peaks
when the laser is on where the counts are above a certain amount. I would check out the Tools menu -> automatic selections -> from Channels.
OK thanks, These are either a series of spots or lines on teeth where we collected data before we were Iolite converts and therefore don't have the laser log files. The data for each sample will be in one ICP-MS files and therefore won't contain discrete spot IDs. Still it seems like from what your saying that we still might be able to do basic peak identification, baseline subtraction and peak integration quicker than just pulling the data into excel and doing it manually?
bpjackso might be able to do basic peak identification, baseline subtraction and peak integration quicker than just pulling the data into excel and doing it manually?
OMG yes, it will be so much easier to do this in iolite than Excel! 
To select baselines, I would go to Tools -> Automatic Selections -> From Channels; add a criterion by clicking the + button in the top left, and then I would try using TotalBeam as the channel, and the comparitor to 'LessThan' and choose some appropriate value (e.g. 10,000 CPS? You can zoom in on your baseline intervals to see what sort of counts you're getting and set a value just above that). This basic process is described in the U-Pb tutorial here (you can ignore everything after selecting the baselines as it's not relevant here).
Then for the peaks, the trouble you might have is differentiating between reference materials and samples. If you're analyzing teeth, I would try creating a criterion based on Ca43 being above a certain value, using the 'GreaterThan' comparator. You have two ways you could do it here: select all ablations and move each of the reference materials ablations to their own group (in the Selections Browser). Or you could find some element (or ratio of elements) that is unique to the reference materials. Then use that as a criterion in the automatic selections as described above.
If you need to use the ratio between two channels, you can run the Trace Elements DRS without having selected your Ref Mats. The DRS will go as far as it can, which will include subtracting the baselines, and ratioing channels. You can then use these ratio channels in the Automatic Selections tool as described above.
If you have any troubles, please just let us know
5 months later
- Edited
I am having the same issue - new to iolite and have multiple individual csv files of data from our Agilent (background, stds, samples) but no log file. Curious, how does one create a log file? Is this something every laser software should do? I'm assuming it comes off a laser software (i.e., ours is Chromium by Teledyne Cetac) and not the ICP-MS Agilent file?
And is it still quicker (and possible) to use iolite with multiple csv files vs doing manually in excel... I think so (anything is faster than that)....
- Edited
Hi @ramorri ,
Log files are created by the laser control software. I think almost all new laser systems do create laser log files, although you might have to turn the feature on, and/or find where the log files are stored. There is some info on how to get your laser logs from Chromium here.
You can definitely still import your data into iolite as a series of individual files. In that case, you can just use the mass spec files that appear in the top half of the Samples Browser to create your selections. The only difference between using mass spec samples and laser log files samples is that the former usually have some amount of background measurement before and after the laser switches on/off. You can remove these intervals when making your selections using the crop values in the Make Selection dialog.
If that doesn't make sense, or if you have any other questions, please just let me know.
-Bence
thank you!!