Reading/Converting Bruker's MALDI-FTICR .d file

[YonghuiDong]

Hi Sebastian,

I would like to use MALDIQuant to analyse Bruker's MALDI-FTICR data. But I don't know how do I convert the raw file to mzML file or other MALDIquantForeign supported format. Or will MALDIquantForeign support such data type?

Here I upload a compressed sample data. The acquired data is basically a folder, which contains various files in it. It can be opened with Bruker's DataAnalysis software, and can be exported to, for instance, .xml or .ascii file. But the software does not support exporting to mzML format.

Here I attached one example data, could you please help?
WT.d.zip

Thanks a lot.

Dong

[sgibb]

I never used FTICR data. Isn't the ascii file a 2 column text file that could be imported?

[YonghuiDong]

@sgibb I have tried with the .ascii file. I have waited for more than 1 hour and the importing process still didn't finish.

Dong

[sgibb]

Could you attach an example .ascii file? 12.09.2020 20:55:59 Dong <notifications@github.com>:

…

@sgibb[https://github.com/sgibb] I have tried with the .ascii file. I have waited for more than 1 hour and the importing process still didn't finish. Dong — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub[#31 (comment)], or unsubscribe[https://github.com/notifications/unsubscribe-auth/AAN6MWYCQB7HF7KDG2TU5CDSFO73LANCNFSM4QLSM5MQ]. [https://github.com/notifications/beacon/AAN6MW2RTDQ4XZSEX3SFXKTSFO73LA5CNFSM4QLSM5M2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFE362GQ.gif]

[YonghuiDong]

Hi Sebastian,

Sorry for my late reply. I have checked the converted .ascii file. It is a one row file, not a two-column (mz-intensity) file. That's why I failed to read it with MALDIquantForeign.

The Bucker software DataAnalysis allows to convert raw .d file to a xy format file, which is a two-column (mz-intensity) text file.

Here I send you one example of the converted file.

test_xy_format.zip

Thanks a lot for your help.

Dong

[sgibb]

You could import this file by using the importTab function and specify the pattern (file name pattern/extension) and sep (field separator) arguments:

library("MALDIquantForeign")
s <- importTab("test.xy", pattern = "\\.xy", header = FALSE, sep = " ")
plot(s[[1]])