[!CAUTION] This nf-core repo has been archived. Development of the quantms pipeline continues at the bigbio repository.
nf-core/quantms is a bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS). Currently, the workflow supports three major MS-based analytical methods: (i) Data dependant acquisition (DDA) label-free and Isobaric quantitation (e.g. TMT, iTRAQ); (ii) Data independent acquisition (DIA) label-free quantification (for details see our in-depth documentation on quantms).
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website. This gives you a hint on which reports and file types are produced by the pipeline in a standard run. The automatic continuous integration tests on every pull request evaluate different workflows, including peptide identification, quantification for LFQ, LFQ-DIA, and TMT test datasets.
nf-core/quantms allows uses to perform analyses of three main types of analytical mass spectrometry-based quantitative methods: DDA-LFQ, DDA-ISO, DIA-LFQ. Each of these workflows share some processes but also includes their own steps. In summary:
thermorawfileparser
)comet
and/or msgf+
percolator
openms fdr tool
luciphor
proteomicsLFQ
proteomicsLFQ
pmultiqc
MSstats
thermorawfileparser
)comet
and/or msgf+
percolator
openms fdr tool
luciphor
IsobaricAnalyzer
ProteinInference
or Epifany
for bayesian inference.ProteinQuantifier
pmultiqc
MSstats
thermorawfileparser
)convert_dotd
to truedia-nn
pmultiqc
A graphical overview of suggested routes through the pipeline depending on context can be seen below.
:::note
If you are new to Nextflow and nf-core, please refer to this page on how
to set-up Nextflow. Make sure to test your setup
with -profile test
before running the workflow on actual data.
:::
First, find or create a sample-to-data relationship file (SDRF).
Have a look at public datasets that were already annotated here.
Those SDRFs should be ready for one-command re-analysis and you can just use the URL to the file on GitHub,
e.g., https://raw.githubusercontent.com/bigbio/proteomics-sample-metadata/master/annotated-projects/PXD000396/PXD000396.sdrf.tsv
.
If you create your own, please adhere to the specifications and point the pipeline to your local folder or a remote location where you uploaded it to.
The second requirement is a protein sequence database. We suggest downloading a database for the organism(s)/proteins of interest from Uniprot.
Now, you can run the pipeline using:
nextflow run nf-core/quantms \
-profile <docker/singularity/.../institute> \
--input project.sdrf.tsv \
--database database.fasta \
--outdir <OUTDIR>
:::warning
Please provide pipeline parameters via the CLI or Nextflow -params-file
option. Custom config files including those
provided by the -c
Nextflow option can be used to provide any configuration except for parameters;
see docs.
:::
For more details and further functionality, please refer to the usage documentation and the parameter documentation.
The nf-core/quantms pipeline comes with a stand-alone full documentation including examples, benchmarks, and detailed explanation about the data analysis of proteomics data using quantms.
To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.
nf-core/quantms was originally written by: Chengxin Dai (@daichengxin), Julianus Pfeuffer (@jpfeuffer) and Yasset Perez-Riverol (@ypriverol).
We thank the following people for their extensive assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
For further information or help, don't hesitate to get in touch on the Slack #quantms
channel (you can join with this invite).
If you use nf-core/quantms for your analysis, please cite it using the following doi: 10.5281/zenodo.7754148
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md
file.
You can cite the nf-core
publication as follows:
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.