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Messages - cagakan

MS-DIAL / peak areas and intensities are much lower than when looking at them in SCIEXOS

March 11, 2024, 04:29:03 AM

When processing WIFF2 files from Sciex Instruments in MSDIAL the peak areas and intensities are much lower than when looking at them in SCIEXOS.
Does anyone know the reason?
Cheers.
Cagakan

MS-DIAL / Sciex WIFF files

April 04, 2023, 03:17:50 AM

Hi all,
As you might know SCIEX records its data files in *.wiff or *.wiff2 files. And sometimes you can add up multiple runs in a single *.wiff file. (attached as an image with the post)

So the MS-DIAL still process even though there are 2 files. Do you know how does it process? Merges them? or processing the only first one only?
Cheers.
Cagakan

MS-DIAL / Re: Colors of dots for metabolomics meaning?

April 04, 2023, 03:08:02 AM

Thank you very much I didnt see you answer until today since I found it out later

cheers.
Cagakan

MS-DIAL / Colors of dots for metabolomics meaning?

January 09, 2023, 05:52:25 AM

Hi guys I have a quick question.
Normally when we run lipidomics analysis color codes of the dots indicate the lipid classes. Is it the same way in metabolomics? That are the different colors mean ?
Thanks for your help and have a great year!

MS-DIAL / Retention Time similarity score in MSDIAL

May 02, 2022, 12:42:19 PM

Hi All,
I have a quick question. I am struggling to understand how the RT similarity function of MSDIAL is working. Do we need to use the same gradient explained in `A lipidome atlas in MS-DIAL 4` article?
If we didn't use the same gradient does it make any sense do use the Retention time similarity function?
Have all the retention time data embedded to `Msp20210527163602_converted.lbm2` from the paper?
Thanks for your help!
Cheers.
Cagakan

Mass spectrometers / Re: QTRAP parameters for lipidomics

August 19, 2016, 07:23:43 AM

hey guys can I recommend my protocol paper here for nanomate-Qtrap5500 experiments.
If you cant download just give your email to me then I can send you the pdf. Cheers
http://link.springer.com/protocol/10.1007%2F978-1-62703-487-6_1

Compound identification / pSRM with Q-exactive

February 08, 2014, 06:50:12 AM

Dear Sir,
I am a PhD student at Heidelberg, and currently I am working on nLC-Exactive to quantify the sphingosine bases.
My questions is while its very simple to create a MRM method with the Q-trap instruments, I dont know how establish this method with Q-E,
Mass transition
C17Sph 286/268 7.2
Sph 300/282 7.5
DHSph 302/284 7.6
S1P 380/264 8.7
DHS1P 382/284 9.0
C17S1P 366/250 8.2

Should I choose Targeted - SIM or data dependent?
I would appreciate if someone could share his/her experiences.

with my best regards.

Cagakan