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Shimadzu 8060RX lcd contains no usable data

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Shimadzu 8060RX lcd contains no usable data Wesley Vermaelen  2024-10-22 22:39
 

Hi,
I've been using Skyline to process data from our Shimadzu 8060NX for a while now and everything works well.
Recently we acquired a new Shimadzu 8060RX but for some reason when I import the results from this machine an error occurs: "The sample contains no usable data".
When I use labsolutions from Shimadzu there is clearly data in the file.

When I use SeeMS from ProteoWizard there is also no data to be seen.

Do you have any idea what is going on here?

I have included two files, one from 8060NX that works and one from the 8060RX that doesn't work. These are similar analysis.

I am very grateful for your help.
Wesley.
 
 
Wesley Vermaelen responded:  2024-10-30 17:00

Hi,
I've noticed that the versions of labsolutions and labsolutions Insight on the 8060RX is newer (v 5.128, v 4.2.SP1).

While the versions on the 8060NX is v5.120, 4.0.SP2 respectively.

As such, I cannot open files run on the RX, on the NX.

Is this a known problem? Is this going to be fixed?

Wesley.
 
Matt Chambers responded:  2024-10-31 12:05

Thanks for the report. I've just merged a fix with updated Shimadzu DLLs that work with your RX file. It'll be included in the next Skyline-daily.
 
Wesley Vermaelen responded:  2024-10-31 15:22

Hi Matt,
Thank you very much!

Wesley
 
Wesley Vermaelen responded:  2025-07-21 21:10

Hi,
We are still having problems uploading Shimadzu .lcd files to a Shimadzu 8060RX.

The peaks shown by Skyline do not look like the peaks shown by Postrun Analysis (from Shimadzu). The signal is a lot lower.

We tried to convert the files to MzML but skyline but this doesn't always work. We get an error uploading the file or "Chromatogram information unavailable" for some compounds, plus it makes the file about 20 times bigger.

I have included two pictures showing a cortisol MRM peak in Skyline and in Postrun Analysis. And the original lcd file.

I hope it is somewhat clear.

Wesley
 
Nick Shulman responded:  2025-07-21 21:38
Wesley,

Can you send us your Skyline document?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url

It would probably also be helpful if you could send us the .mzML file that you created which was causing other problems for you.
-- Nick
 
Wesley Vermaelen responded:  2025-07-21 22:06

Here is the .zip file.

I have uploaded the mzML file to the files.url.

The error we get is:
"At 3:04 PM:
Failed importing results file 'D:\LabSolutions\DATA\2025\20250715_SterHorm_StrigLact_test\SH_STD_01uL.mzML'.
Times (1283) and intensities (1284) disagree in point count."

Thank you,
Wesley.
 
Nick Shulman responded:  2025-07-21 23:22
Thank you for uploading that .mzML file and your Skyline document.
The error about Times and Intensities disagreeing in point count seems to be a bug in Skyline.
There are spectra in the .mzML file which represent SRM chromatograms.
Skyline is supposed to be able to handle that, but Skyline seems to be confused about one spectrum that maybe does not have all of the intensities that it was expecting.
I believe this bug will end up being straightforward to fix as soon as I figure out exactly what is going on.

Do you also want us to fix the problem where the chromatogram from the .lcd file does not look like your other screenshot? I do not know what might be going on there, but I could try to find someone else to look at that.
-- Nick
 
Wesley Vermaelen responded:  2025-07-21 23:35

Hi Nick
thanks for looking at it.

Well the main issue is the fact that the chromatogram doesn't look like the chromatogram given by the vender software.

We would like to keep using the .lcd files in stead of converting them.

As stated in the beginning of this thread, we also have a Shimadzu 8060NX, and uploading the original Shimadzu .lcd files works perfectly there.

So if you can find someone that can have a look at it, that would be great.

Thanks again,
Wesley
 
Matt Chambers responded:  2025-07-22 09:50

Hi Wesley,

We'll need the LCD file to figure out why it's giving a different result than the Shimadzu mzML.
 
Wesley Vermaelen responded:  2025-07-22 16:35

Hi,
The .lcd file can be found in a previous reply.

I will send it again.

Thanks.
 
Matt Chambers responded:  2025-08-06 13:45

Sorry for the delay. I'm looking at this file and I don't see anything close to the intensities in the PostrunAnalysis picture you attached above. This is true whether I look at the SRM chromatograms from pwiz opening the LCD directly, or when looking at the spectra in the mzML file you provided.

In the SH_STD_DER_Method.LCD file for 363/121, I see:
time intensity
2.41 0
2.42 12594
2.43 38977
2.44 33806
2.45 27026
2.46 29162
2.48 31818
2.49 31260
2.50 4251
2.51 0

In the SH_STD_01uL.mzML file for 363/121, I see:
2.34 6224
2.36 21506
2.38 48729
2.39 74223
2.41 97314
2.43 110061
2.45 110663
2.46 101618
2.48 83233
2.50 57127
2.52 35054
2.53 21990
2.55 18119
2.57 14427
2.58 10536
2.60 8774

Both of those are way off the apex intensity of 1.6e6 in your PostrunAnalysis. It would be interesting to have the same mzML file for the LCD file you provided. Since it's a different run I can't expect the numbers to really be comparable. But I must assume that either you're looking at a different file in PostrunAnalysis or that it's been postprocessed somehow.
 
Wesley Vermaelen responded:  2025-08-06 21:08

Hi,
I have include the mzML file for the SH_STD_DER_Method.LCD (It is zipped because otherwise it is too big)

And I have included the comparison of LCD vs MzML in the picture for transition 363.22 > 121.00 (Cortisol)
SH_STD_DER_Method = LCD
SH_STD_DER_Method2 = MzML

The results for SH_STD_01uL.MzML do match the LCD File if I open the LCD file in Postrun Analysis (Shimadzu). But if I open this LCD file in Skyline the peak signal is 9500, more than 10 times less than the Postrun Analysis result.

The goal here is to be able to upload the original LCD file (without converting to mzML format) and get the same intensity peak shape as the original software.

I thank you again,
Wesley
 
Matt Chambers responded:  2025-08-07 09:22

Thanks for the file. I'm now able to reproduce the superior spectrum-based signal from the LCD file. We generally try to read MRM data using vendors' chromatogram-centric APIs but for some reason on this instrument/file the spectrum-centric and chromatogram-centric APIs are seriously out of sync. I will ask Shimadzu what's going on here.