Dear quantms community,
The quantms team has been working hard to build a fully independent pipeline for DIA-NN and DIA analysis. This effort is driven by two main reasons:
1. Keeping pace with DIA-NN's growth
DIA-NN has expanded significantly in recent years and will continue to do so — with new versions, command-line options, formats, and analysis modes. When we first integrated DIA-NN into quantms (starting with v1.8.1), only a handful of options were available. Today, the scope is much larger. A dedicated pipeline means users no longer need to navigate unrelated options from other workflows and can have full, fine-grained control over their DIA-NN analyses.
2. Better scalability and focus
The parallel version of DIA-NN scales well in HPC environments, and a standalone pipeline makes it easier to use independently of DDA, TMT, or other quantms workflows. It also opens the door to DDA analysis support in the future.
The new pipeline maintains the same quantms ecosystem for inputs and outputs — SDRF, MSstats, and in the future QPX — alongside native DIA-NN output formats.
Roadmap
- quantmsdiann v1.0.0 was released last week: https://github.com/bigbio/quantmsdiann. It supports all features currently available in quantms and lets you configure any DIA-NN version you wish to use.
- quantmsdiann v2.0.0 is in progress and will add DDA search support and compatibility with the newly released DIA-NN 2.5.0.
- A new workflow documentation site is live at https://quantmsdiann.quantms.org/, making it easier to understand parameters and get started.
What this means for quantms
We have paused the integration of new DIA-NN features into the main quantms pipeline. In the next quantms release, the DIA-NN analysis branch will be removed, with a clear warning directing users to quantmsdiann. Users who wish to stay on the current integration can continue using previous versions of quantms.
A big thank you to all contributors: @an-altosian, @enryH, @jpfeuffer, @jspaezp, @timosachsenberg, @yueqixuan, @daichengxin, and the entire quantms community. Special thanks to @vdemichev for his continued support of the quantms project.
Best,
Yasset
Dear quantms community,
The quantms team has been working hard to build a fully independent pipeline for DIA-NN and DIA analysis. This effort is driven by two main reasons:
1. Keeping pace with DIA-NN's growth
DIA-NN has expanded significantly in recent years and will continue to do so — with new versions, command-line options, formats, and analysis modes. When we first integrated DIA-NN into quantms (starting with v1.8.1), only a handful of options were available. Today, the scope is much larger. A dedicated pipeline means users no longer need to navigate unrelated options from other workflows and can have full, fine-grained control over their DIA-NN analyses.
2. Better scalability and focus
The parallel version of DIA-NN scales well in HPC environments, and a standalone pipeline makes it easier to use independently of DDA, TMT, or other quantms workflows. It also opens the door to DDA analysis support in the future.
The new pipeline maintains the same quantms ecosystem for inputs and outputs — SDRF, MSstats, and in the future QPX — alongside native DIA-NN output formats.
Roadmap
What this means for quantms
We have paused the integration of new DIA-NN features into the main quantms pipeline. In the next quantms release, the DIA-NN analysis branch will be removed, with a clear warning directing users to quantmsdiann. Users who wish to stay on the current integration can continue using previous versions of quantms.
A big thank you to all contributors: @an-altosian, @enryH, @jpfeuffer, @jspaezp, @timosachsenberg, @yueqixuan, @daichengxin, and the entire quantms community. Special thanks to @vdemichev for his continued support of the quantms project.
Best,
Yasset