2_Raw_HRMS_data.qmd

---
title: "Raw HRMS Data"
editor_options: 
  chunk_output_type: console
---

# Raw HRMS Data

## A look into the mzml data structure

<https://rformassspectrometry.github.io/book/sec-raw.html>

Loading libraries

```{r}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("tidyverse")
BiocManager::install("factoextra")
BiocManager::install("msdata")
BiocManager::install("mzR")
BiocManager::install("rhdf5")
BiocManager::install("rpx")
BiocManager::install("MsCoreUtils")
BiocManager::install("QFeatures")
BiocManager::install("Spectra")
BiocManager::install("ProtGenerics")
BiocManager::install("PSMatch")
BiocManager::install("pheatmap")
BiocManager::install("limma")
BiocManager::install("MSnID")
BiocManager::install("RforMassSpectrometry/SpectraVis")

library(Spectra)

```

Open test mzml file (Waters MSe)

```{r}

# This Waters MSe does not have totIonCurrent 
# mzf <- "D:/OneDrive - Linköpings universitet/Raw_data/Dust_Florian/LC/LC_pos_mzML/QC_rep2.mzML"

# Agilent qtof data contain totIonCurrent
mzf <- "C:\\Users\\vicer06\\OneDrive - Linköpings universitet\\Documents\\01_Projects\\01_VION_HRMS_MSConvert_Processing_2024\\Test_Spectra_Function_R\\Drugstd-200ppb_1_A,3_1.mzML"

sp <- Spectra(mzf)
```

Checking metainfo

```{r}
#plotting individual spectra
plotSpectra(sp[2784]) #MS1
plotSpectra(sp[2785]) #MS2


with(spectraData(filterMsLevel(sp, 1)),
     plot(rtime, totIonCurrent, type = "l"))
abline(v = rtime(sp)[2784], col = "red")

ms_2 <- filterPrecursorScan(sp, 2784)
```