Import_MSdatasets.qmd

# Read MS datasets into R

Pre-processed MS datasets refers to data exported from MS rawdata processing software, such as Agilent MassHunter, Sciex Multiquant, and open-source tools as MRMkit and Skyline. These datasets usually contain peak/signal intensities and associated data such as retention time, FWHM, as well as information about the sample.

The R package [SLINGtools](https://github.com/SLINGhub/SLINGtools) provided helper functions to import data files obtained from different tools.

## Import peak areas from Agilent MassHunter CSV file

![](images/paste-B702CE09.png)

```{r}
#| label: read-areas-MassHunter-CSV
library(SLINGtools)
data_file_path <- here::here("data/Testdata_Lipidomics_MHQuant_Detailed_V2.csv")
d_wide <- SLINGtools::read_MassHunterCSV_wide(data_file_path, field = "Area")
print(d_wide)
```

## Import all data from an Agilent MassHunter CSV file

Detail [MassHunter Quant](https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/quantitative-analysis).

![](images/paste-A1421EC0.png)

```{r}
#| label: read-full-MassHunter-CSV
data_file_path <- here::here("data/Testdata_Lipidomics_MHQuant_Detailed_V2.csv")
d_all_long <- SLINGtools::read_MassHunterCSV(data_file_path)
print(d_all_long)
```