nf-PTM-Analyzer is a Nextflow pipeline that executes the PTM-Analyzer programs, which enable statistical analysis and quantitative exploration of proteomics data related to post-translational modifications (PTMs).
nf-PTM-Analyzer was developed by the Cardiovascular Proteomics Lab/Proteomic Unit at The National Centre for Cardiovascular Research (CNIC, https://www.cnic.es).
This application is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) License. For further details, read the https://creativecommons.org/licenses/by-nd/4.0/.
Before you begin, ensure you have met the following requirements:
- A Linux operating system is needed on your machine.
If you are using a Windows operating system, refer to the section Install WSL on Windows to set up a Linux operating system on your Windows machine.
For more information, read the How to install Singularity section.
For more information, read the How to install Nextflow section.
For more information, read the How to install Git section.
Export an environment variable to define the version:
export PIPELINE_VERSION=1.6
Note: The list of releases is located on the releases page.
You can clone the latest release directly using git with the following command:
git clone https://github.com/CNIC-Proteomics/nf-PTM-Analyzer.git --branch ${PIPELINE_VERSION} --recursive
With the --recursive parameter, the submodules repositories are cloned as well.
Export an environment variable to define the version of singularity image:
export IMAGE_VERSION=1.5
Note: The list of releases is located on the singularity repository page.
Navigate to the backends folder:
cd nf-PTM-Analyzer/backends
You need to download the Singularity image for the pipeline, ensuring version compatibility with the Nextflow pipeline. See the above versions section:
singularity pull --arch amd64 library://proteomicscnic/next-launcher/ptm_analysis:${IMAGE_VERSION}
You might see warning messages like the following. You can discard or ignore them:
WARNING: failed to get key material: 404 Not Found: entity not found
WARNING: integrity: signature object 5 not valid: openpgp: signature made by unknown entity
WARNING: Skipping container verification
Create a symbolic link
ln -s ptm_analysis_${IMAGE_VERSION}.sif ptm_analysis.sif
Input files for PTM-Analyzer, derived from the quantification results of iSanXoT [1] and the PDM table from the PTM-compass [2].
The samples originate from heart tissue, based on the study by Bagwan N, Bonzon-Kulichenko E, Calvo E, et al. [3].
- Download sample files
cd samples && \
wget https://zenodo.org/records/17141424/files/heteroplasmic_heart.zip?download=1 -O heteroplasmic_heart.zip && \
unzip heteroplasmic_heart.zip && \
cd ..
- Execute the pipeline using iSanXoT report (q_all) and PDM table from PTM-compass as inputs:
nextflow \
-log "/tmp/nextflow/log/nf-ptm-analyzer.log" \
run main.nf \
-profile singularity \
--quant_file "samples/heteroplasmic_heart/inputs/q_all.tsv" \
--pgm_file "samples/heteroplasmic_heart/inputs/DMTable_PeakAssignation_FDRfiltered_DM0S_PA_T_PeakAssignation_SS_Heart_FDR_PDMTable_GM_J_PGM_Table_pgmFreq.tsv" \
--params_file "samples/heteroplasmic_heart/inputs/params_nf.yml" \
--compa_file "samples/heteroplasmic_heart/inputs/limma_comparisons.tsv" \
--qmeta_file "samples/heteroplasmic_heart/inputs/myMitocarta.tsv" \
--outdir "samples/heteroplasmic_heart/results" \
-resume
The computational experiment was performed on a virtualized environment running under Windows Subsystem for Linux 2 (WSL2). The software and hardware configuration were as follows:
- Operating system: Ubuntu 22.04.5 LTS (Jammy Jellyfish), kernel version 6.6.87.2
- Processor: Intel Xeon E5-2670 (Sandy Bridge) with 16 physical cores and 32 threads (Hyper-Threading enabled), base frequency ~2.6 GHz, cache hierarchy: L1 = 1 MB, L2 = 4 MB, L3 = 20 MB
- Memory (RAM): 39 GiB
- Storage: ~2 TiB available capacity
The execution trace for the sample dataset was generated using the nextflow command above.
The trace log shows the execution of each module along with the corresponding execution time.
You can download the input files for this liver sample, derived from the study by Bagwan N, Bonzon-Kulichenko E, Calvo E, et al. [1] at the following URL:
https://zenodo.org/records/17141424/files/heteroplasmic_liver.zip?download=1
To execute the pipeline, follow the same steps as in Sample 1.
You can download the input files for this sample from the following URL:
https://zenodo.org/records/17141424/files/heteroplasmic_muscle.zip?download=1
To execute the pipeline, follow the same steps as in Sample 1.
For more information about the program version included within the Singularity version, refer to the changelog for the current version.
[1] Rodríguez, Jose Manuel et al. iSanXoT: A standalone application for the integrative analysis of mass spectrometry-based quantitative proteomics data. Computational and structural biotechnology journal vol. 23 452-459. 26 Dec. 2023, doi: https://doi.org/10.1016/j.csbj.2023.12.034
[2] Cristina A. Devesa, Rafael Barrero-Rodríguez, Andrea Laguillo-Gómez, et al. Integrative multi-layer workflow for quantitative analysis of post-translational modifications. bioRxiv 2025.01.20.633864; doi: https://doi.org/10.1101/2025.01.20.633864
[3] Bagwan N, Bonzon-Kulichenko E, Calvo E, et al. Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy. Cell Reports. 2018;23(12):3685-3697.e4. https://doi.org/10.1016/j.celrep.2018.05.080