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:
artMS performs the different analyses taking as input the following files:
evidence.txtfile: The output of the quantitative proteomics software package
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
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:
If the outcome is
>= 3.6.0, congratulations! you can move forward
Two options to install
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.
(Warning: not stable, but it has the latest)
Assuming that you have an
R (>= 3.6) version running on your system, follow these steps:
Check that it is up and running by checking, for example, the documentation of the qc function
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")
Once the QC is done, go to the folder
"/path/to/your/working/directory/" and check out all the generated QC (pdf) files.
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.
There are multiple options:
Do you need to remember the basics of markdown? Check out this fantastic link.
The vignette can also be accessed at https://artms.org