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lipidomics.qmd
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lipidomics.qmd
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---
title: "Lipidomics"
editor:
markdown:
wrap: 72
---
See [Figure 2](index.qmd#fig-2) for the meanings of the abbreviations used in this chapter.
## 1. DI-MS/MS (DDA)
A project dealing with data dependent DI-MS acquisition in combination
with the in silico retention time and MS/MS databases for lipids is
demonstrated.
This tutorial uses 15 demonstration files which are downloadable from
the below link.\
[http://prime.psc.riken.jp/compms/msdial/download/demo/dims.zip](http://prime.psc.riken.jp/compms/msdial/download/demo/dims.zip)
**Experiment summary:**\
The direct infusion MS data analyzing plasma, white adipose tissue (WAT), muscle, and liver of mice in addition to the procedure blank samples.
The MS/MS spectrum was acquired by information dependent acquisition (IDA) mode of SCIEX meaning data dependent acquisition (DDA).
### 1-1 Starting up your project
{#fig-1}
)
(4).](images/Chapter2/Fig2%20Importing%20raw%20data%20files%20and%20setting%20up%20the%20measurement%20parameters.png){#fig-2}
To see the above operation in YouTube, check out the following
{{< video https://www.youtube.com/watch?v=Zo7qBcduc1E >}}
## 2. DI-MS/MS (MSall)
A project dealing with MSall DI-MS acquisition in combination with the
in silico retention time and MS/MS databases for lipids is demonstrated.
Additionally, you can watch our tutorial video:
{{< video https://www.youtube.com/watch?v=YiAj0K37-CE&ab_channel=MS-DIALproject >}}
## 3. DI-MS/MS (DDA)
A project dealing with DDA DI-MS acquisition in combination with the
in silico retention time and MS/MS databases for lipids is demonstrated.
Additionally, you can watch our tutorial video:
{{< video https://www.youtube.com/watch?v=Zo7qBcduc1E&ab_channel=MS-DIALproject >}}
## 4. LC-MS/MS (SWATH)
A project dealing with data independent LC-MS acquisition using the
Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH-MS)
in combination with the in silico retention time and MS/MS databases for
lipids is demonstrated.
### Input Data
This tutorial uses 23 demonstration files which are downloadable from <http://prime.psc.riken.jp/archives/data/DropMet/019/20140809_MSDIAL_DemoFiles_Swath(abf).zip>.
The experimental protocol is described in previous research: <http://www.nature.com/nmeth/journal/v12/n6/abs/nmeth.3393.html>.
#### Experiment summary:
Liquid chromatography: total 15 min run per sample with Waters Acquity UPLC CSH C18 column (100×2.1 mm; 1.7 μm).
Mass spectrometer: SWATH method with negative ion mode.
- MS1 accumulation time, 100 ms
- MS2 accumulation time, 10 ms
- Collision energy, 45 V
- Collision energy spread, 15 V
- Cycle time, 731 ms
- Q1 window, 21 Da
- Mass range, m/z 100-1250
- Modifier, Ammonium formate (HCOONH4)
Additionally, you can watch our tutorial video:
{{< video https://www.youtube.com/watch?v=HV-e9wG9WRo&ab_channel=MS-DIALproject >}}
## 5. LC-MS/MS (Hybrid MS-DDA/SWATH)
A project dealing with LC-MS/MS (Hybrid MS-DDA/SWATH) acquisition in combination with the in silico retention time and MS/MS databases for lipids is demonstrated. \
Hybrid MS-DDA/SWATH is a novel strategy combining DIA and DDA in fast LC-MS-based analytical batches, intending to increase annotation rates.
The input data to the workflow is located in [](https://doi.org/10.5281/zenodo.10590080). \
See the Zenodo dataset for description of the input data.
### The Workflow
1. Download and unzip the tutorial dataset.
2. Add the LBM2 file to the MS-DIAL folder. \
NOTE: Exclude the original LBM2 format. The program accepts only one LBM/LBM2 file in the MS-DIAL folder.
4. Start up a new project in MS-DIAL.
3. Follow the YouTube video below to operate the MS-DIAL5 GUI.
{{< video https://www.youtube.com/watch?v=IGPQMCW1FPw >}}
4. The output is obtained as *.mdproject.
### Reference
See below for the details of "Hybrid MS".\
[K. Tokiyoshi et al. Anal Chem, 96, 991-996. 2024](https://doi.org/10.1021/acs.analchem.3c04400)
## 6. LC-MS/MS (EAD) - deep structural lipid annotation
The input data to the workflow is located in [](https://doi.org/10.5281/zenodo.10616947).
See the Zenodo dataset for description of the input data.
Additionally, you can watch our tutorial video:
{{< video https://www.youtube.com/watch?v=uyD1rmSZKuw >}}
## 7. DI-IM-MS/MS
A project dealing with DI-IM-MS acquisition in combination with the in silico retention time and MS/MS databases for lipids is demonstrated.
Additionally, you can watch our tutorial video:
{{< video https://www.youtube.com/watch?v=-LQiiEk-DBw >}}
## 8. LC-IM-MS/MS(SWATH)
A project dealing with LC-IM-MS/MS acquisition in combination with the in silico retention time and MS/MS databases for lipids is demonstrated.
Additionally, you can watch our tutorial video:
{{< video https://www.youtube.com/watch?v=4R5Tmaic7A8 >}}