Lipidomics

See Figure 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

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

Figure 1: Figure 1 Starting up a project in MS-DIAL. First open the MSDIAL.exe file in the downloaded folder (1). Click on new project (2). You can name your project according to your preferences (3). Browse to the location of your experimental files (here your processing files will be also stored) (3). Click next and then continue to the second left side bar “Raw measurement files”. Here click browse to access your raw data files (4).

Figure 2: Figure 2 Importing raw data files and setting up the measurement parameters. Change the type of file according to your vendor format and select raw data files which you want to import (note: the data files will be imported according to the alphabetical order) (1). After inserting your raw data files, you will be able to further assign identifiers to your measurements by sample type (Sample, Standard, QC, Blank), class ID (according to your experimental setup), and you can also set the batch (if you analyzed multiple batches), analytical order, dilution factor, or possibly exclude some samples from further data processing (2). It is advisable to select the blanks and QC samples (if measured) to be able to use all functions of MS-DIAL (such as blank filtering or LOWESS signal correction based on QCs) (3). After clicking next and selecting the “Measurement parameters” in the left side tab you can specify your analytical setup according to this figure (more details are provided in the intruduction section) (4).

To see the above operation in YouTube, check out the following

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:

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:

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:

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 .
See the Zenodo dataset for description of the input data.

The Workflow

Download and unzip the tutorial dataset.
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.
Start up a new project in MS-DIAL.
Follow the YouTube video below to operate the MS-DIAL5 GUI.