10_12_mzR.Rmd

### mzR

The `mzR` package is a powerful tool for analyzing large raw data files in proteomics research. It offers a direct interface to the [proteowizard](http://proteowizard.sourceforge.net/) code base, which is a widely-used software framework for mass spectrometry data analysis. By leveraging a substantial proportion of *pwiz*'s C/C++ code, `mzR` is able to provide fast and efficient parsing of these complex data files.

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+---------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+
| ![](images/05.png){height="68"} | [WEB tutorial](https://lgatto.github.io/2020-02-17-RProt-Berlin/raw-ms-data-mzr-and-msnbase.html)                                           |
|                                 |                                                                                                                                             |
|                                 | [PDF manual](https://bioconductor.org/packages/release/bioc/manuals/mzR/man/mzR.pdf)                                                        |
|                                 |                                                                                                                                             |
|                                 | [Bioconductor](https://bioconductor.org/packages/release/bioc/html/mzR.html)                                                                |
|                                 |                                                                                                                                             |
|                                 | *Chambers, Matthew C., et al. "A cross-platform toolkit for mass spectrometry and proteomics." Nature biotechnology 30.10 (2012): 918-920.* |
+---------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------+

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Read in an \@ref(mzml) mzML converted LCMS data file and check its contents.
```{r, eval=FALSE, warning=FALSE, message=FALSE}
# download the file
url <- "https://raw.githubusercontent.com/jeffsocal/ASMS_R_Basics/main/data/small.mzML"
download.file(url, destfile = "./data/small.mzML")

library(mzR)

ms_dat <- openMSfile("./data/small.mzML")

ms_dat
```

```{r, echo=FALSE, warning=FALSE, message=FALSE}
library(mzR)

ms_dat <- openMSfile("./data/small.mzML")

ms_dat
```

Extract out a specific spectrum.
```{r, warning=FALSE, message=FALSE}
library(tidyverse)

tbl_spec <- peaks(ms_dat, 36) %>% as_tibble()

tbl_spec
```

```{r, warning=FALSE, message=FALSE, fig.width=8, fig.height=3, fig.align='center'}
tbl_spec %>% 
  ggplot(aes(mz, intensity)) + 
  geom_segment(aes(xend = mz, yend = 0))
```

In addition to its parsing capabilities, `mzR` includes a range of useful functions for working with mass spectrometry data. This package supports a wide variety of file formats, and provides functions for reading, writing, and manipulating data in these formats. Furthermore, `mzR` includes features for working with tandem mass spectrometry (MS/MS) data, including functions for spectral processing and peak picking.

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