chenxingqiang / artms

Analytical R Tools for Mass Spectrometry

artMS

Analytical R Tools for Mass Spectrometry

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Overview

artMS is an R package that provides a set of tools for the analysis and integration of large-scale proteomics (mass-spectrometry-based) datasets obtained using the popular proteomics software package MaxQuant. The functions available in artMS can be grouped into 4 major categories:

• Multiple quality control (QC).
• Relative quantification using MSstats.
• Downstream analysis and integration of quantifications (enrichment, clustering, PCA, summary plots, etc)
• Generation of input files for other tools, including SAINTq and SAINTexpress, Photon, and Phosfate

artMS performs the different analyses taking as input the following files:

• evidence.txt file: The output of the quantitative proteomics software package MaxQuant.
• keys.txt (tab-delimited) txt file generated by the user describing the experimental designed (check below to learn how to create it).
• contrast.txt (tab-delimited) txt file generated by the user with the comparisons between conditions to be quantified (check below to learn how to create it).
• config.yaml: a configuration file which enables the customization of a number of parameters for the quantification (and other operations, including QC analyses, charts and annotations). A configuration file template can be generated by running artmsWriteConfigYamlFile()

How to install

We assume that you have both R and RStudio already installed on your system. Please, ensure that your system is running an R version >= 3.6 or otherwise nothing will work (Bioconductor requirement). You can check the R version currently running on your system by executing this command in RStudio:

getRversion()

If the outcome is >= 3.6.0, congratulations! you can move forward

If it is not, then you need to install the latest version of R in your system. After updating to the latest R version, open RStudio and try again getRversion() to make sure it worked.

Two options to install artMS

Official BioConductor releases (recommended)

artMS is available on BioConductor. Run the following lines:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("artMS", version = "3.8")

Why Bioconductor? Here you can find a nice summary of good reasons.

Development version from this repo

(Warning: not stable, but it has the latest)

Assuming that you have an R (>= 3.6) version running on your system, follow these steps:

install.packages("devtools")
library(devtools)
install_github("biodavidjm/artMS")

Check that it is up and running by checking, for example, the documentation of the qc function artmsQualityControlEvidenceBasic:

library(artMS)
?artmsQualityControlEvidenceBasic

Once installed, we suggest you to do a quick test by running the quality control functions using the "evidence" (artms_data_ph_evidence) and "keys" (artms_data_ph_keys) files included in artMS as test datasets.

# First go to a local working directory: several pdfs will be generated
# setwd("/path/to/your/working/directory/")

# And run:
artmsQualityControlEvidenceBasic(evidence_file = artms_data_ph_evidence,
                                  keys_file = artms_data_ph_keys, 
                                  prot_exp =  "PH")

(To learn more about these testing datasets, check the documentation by running ?artms_data_ph_keys or ?artms_data_ph_evidence on the R console)

Once the QC is done, go to the folder "/path/to/your/working/directory/" and check out all the generated QC (pdf) files.

How to Contribute to artMS

artMS is an open source project, therefore you are more than welcome to contribute and make the analysis of Mass Spectrometry data easier and better using this fantastic language and environment for statistical computing and graphics (i.e. R).

There are multiple options:

• Submit issues to this repo reporting problems, bugs, or suggesting new features.
• Fork and make pull requests. To find out more about this option, some very useful guides for beginners can be found here and there (or even beyond)

Tips

Do you need to remember the basics of markdown? Check out this fantastic link.

artMS Help available online

The vignette can also be accessed at https://artms.org