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Messages - AnaCarolina-RosadaSilva

1
MS-DIAL / Re: How to find the internal standard by using MS-DIAL
Hello guys.

In this book chapter we explained how to do that: https://link.springer.com/chapter/10.1007/978-1-0716-2107-3_6#DOI

Basically here is what you need to do:

Create a table with the following information to find the internal standards in data efficiently: Name, m/z (MZ), retention time (RT), Adduct, InChiKey, Formula, Smiles, and Ontology. An example for PC 15:0_18:1(d7) is showed below. Save the table as .txt. Go to Advanced in the “Identification” tab, and select this .txt file. Set 100 min to “Retention time tolerance”, 0.01 Da as “Accurate mass tolerance”, and 80% to “Identification score cut off”.
Name PC 15:0_18:1(d7)
RT 12.75
MZ 775.59531
Adduct [M+Na]+
InChiKey ZEWLMKXMNQOCOQ-GCHPQBSENA-N
Formula C41H73D7NO8P
Smiles [C@](COP(=O)(
  • )OCC[N+](C)(C)C)([H])(OC(CCCCCCC/C=C\CCCCCC([2H])([2H])C([2H])([2H])C([2H])([2H])[2H])=O)COC(CCCCCCCCCCCCCC)=O
Ontology PC 


I hope it helps you!
3
MS-DIAL / LC-MS data with AIF - Agilent 6545i
Hello!

Does anyone have experience analyzing LC-MS with AIF metabolomics data from Agilent 6464i?

I am trying version 5.1.22, it seems that is working but then it just closes without any message.

4
MS-DIAL / Re: MS-Dial lipid RTs: Is there a published LC method RTs are derived from?
Hey Brian.

They have described all the methods that they tested on their paper: https://www.nature.com/articles/s41587-020-0531-2

Also, in the identification tab you can choose to not consider RT, for example:
Retention time tolerance   100 min

I am used to doing that. There are all the parameters to LC-MS data on my published paper (https://doi.org/10.1016/j.foodres.2020.109727).


Best Regards,
Ana Carolina
5
MS-DIAL / Re: How to analyze Agilent 6560 ion mobility AIF data?
Hi.

I have been working with AIF IMS data and to analyse them through MS-DIAL you should check Ion mobility and then data independent MS/MS. In my view, so far MS-DIAL is not able to distinguish the different energy collisions in this system.

Hope it help you.

Should you have more questions, please send me an email:
acarolinarosa.16@gmail.com


Best Regards,
Ana Carolina
6
MS-DIAL / Re: Areas of EquiSplash Lipidomix
Hi. Sorry for my late answer.

Regarding quantification, I would rather normalize areas in excel, because MS-DIAL quantification is better to plasma or tissues samples.
If you need more help please send me an email:

acarolinarosa.16@gmail.com


Best Regards,
Ana Carolina
8
MS-DIAL / Re: MS-DIAL 4.48 for IMS samples (Agilent)
Hi Manuella!
Yes, I am running samples from DIA All ions Agilent 6560 IM-QTOF, though I have not tested this new version yet.
In fact I tried drag and drop the samples but it presented an error.
At the end in the 4.48 version I am able to run 21 samples from positive mode for  around 5 hours and from negative mode 2 hours.
But I will try tomorrow and I can tell you afterwards.

Best,
Ana Carolina
9
MS-DIAL / Areas of EquiSplash Lipidomix
Hi everyone.
I work with green coffee beans, using 15 uL of EquiSplash and 7.5 mg of milled coffee beans.
In the lipidomics workflow I have had difficulties to find the deuterated standards, even though I know that they are there in my raw data. Has everyone had the same problem ?
Do I need to do something to identified these compounds ?


11
MS-DIAL / MS-DIAL 4.48 for IMS samples (Agilent)
Hello.
I am trying to process LC-IM-QTOF data  in the MS-DIAL 4.48, but the time to end has been higher than I was expecting.
I am processing only two lipid samples, because it is only a test. This is my first time with ion mobility, but I have been using MS-DIAL for my first work using lipidomics and orbitrap.

The computer is a desktop with 192 GB of RAM.

Do you have long processing times for ion mobility data ? More than 3-4 hours ?

Thank you.
Ana Carolina Rosa