https://github.com/tnaake/msquality

https://github.com/tnaake/msquality

mass-spectrometry metabolomics proteomics qc r

Last synced: 28 days ago
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• Host: GitHub
• URL: https://github.com/tnaake/msquality
• Owner: tnaake
• Created: 2021-05-21T13:10:53.000Z (over 3 years ago)
• Default Branch: devel
• Last Pushed: 2024-02-21T15:09:45.000Z (10 months ago)
• Last Synced: 2024-10-28T12:44:03.883Z (about 2 months ago)
• Topics: mass-spectrometry, metabolomics, proteomics, qc, r
• Language: R
• Homepage:
• Size: 19.2 MB
• Stars: 7
• Watchers: 2
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md

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README

        
# MsQuality

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![R-CMD-check-bioc](https://github.com/tnaake/MsQuality/workflows/R-CMD-check-bioc/badge.svg)

[![codecov.io](http://codecov.io/github/tnaake/MsQuality/coverage.svg?branch=master)](http://codecov.io/github/tnaake/MsQuality?branch=main)

[![license](http://img.shields.io/badge/license-GPL%20%28%3E=%203%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-3.0.html)

Calculation of QC metrics from mass spectrometry data

## Description

Data quality assessment is an integral part of preparatory data analysis 

to ensure sound biological information retrieval. 

We present here the `MsQuality` package, which provides functionality to calculate

quality metrics for mass spectrometry-derived, spectral data at the per-sample

level. `MsQuality` relies on the [`mzQC`](https://github.com/HUPO-PSI/mzQC) 

framework of quality metrics defined by the Human Proteome 

Organization-Proteomics Standards Intitiative (HUPO-PSI). These metrics 

quantify the quality of spectral raw files using a controlled vocabulary. 

The package is especially addressed towards users that acquire 

mass spectrometry data on a large scale (e.g. data sets from clinical settings 

consisting of several thousands of samples): while it is easier to control 

for high-quality data acquisition in small-scale experiments, typically run

in one or few batches, clinical data sets are often acquired over longer 

time frames and are prone to higher technical variation that is often

unnoticed. `MsQuality` tries to address this problem by calculating metrics that

can be stored along the spectral data sets (raw files or feature-extracted 

data sets). `MsQuality`, thus, facilitates the tracking of shifts in data quality

and quantifies the quality using multiple metrics. It should be thus easier

to identify samples that are of low quality (high-number of missing values,

termination of chromatographic runs, low instrument sensitivity, etc.).

The `MsQuality` package allows to calculate low-level quality metrics that require

minimum information on mass spectrometry data: retention time, m/z values, 

and associated intensities.

The list included in the `mzQC` framework is excessive, also including 

metrics that rely on more high-level information, that might not be readily

accessible from .raw or .mzML files, e.g. pump pressure mean, or rely

on alignment results, e.g. retention time mean shift, signal-to-noise ratio,

precursor errors (ppm). 

The `MsQuality` package is built upon the `Spectra` and the `MsExperiment` package.

Metrics will be calculated based on the information stored in a 

`Spectra` object, thus, the spectral data of each sample should be stored

in one `Spectra` object. The `MsExperiment` serves as a container to 

store the mass spectral data of multiple samples. `MsQuality` enables the user

to calculate quality metrics both on `Spectra` and `MsExperiment` objects. 

## Contact 

You are welcome to 

 * write a mail to  

 * submit suggestions and issues: 

 * send a pull request:  

## Install

`MsQuality` is available via Bioconductor. To install the package, users can

either install from the 

[devel branch](https://bioconductor.org/packages/devel/bioc/html/MsQuality.html) 

or from the current 

[RELEASE branch](https://bioconductor.org/packages/release/bioc/html/MsQuality.html).

To install `MsQuality`, you have first to install the 

[`BiocManager`](https://www.bioconductor.org/install/) and

[remotes](http://cran.r-project.org/web/packages/cran/index.html) 

package: 

```r

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

if (!requireNamespace("remotes", quietly = TRUE))

    install.packages("remotes")

```

Install the `MsQuality` package then via

```r

## to install from Bioconductor

BiocManager::install("MsQuality")

## to install the development version from GitHub

BiocManager::install("tnaake/MsQuality")

```