pLink3-HD Version 3.1.8

3.1.8 - 2026-09-17

New Features

• Added FDR control at the residue-pair-group (Residue Pairs (Group)) and protein-protein-interaction-group (PPIs (Group)) levels, analogous to protein grouping in conventional proteomic identification.
• At the residue-pair-group and PPI-group FDR levels, ambiguous results can now be reported, including cases where peptide-to-protein mapping is non-unique, i.e., where a peptide sequence is shared by multiple proteins. In contrast, the existing unique-residue-pair (Residue Pairs (Unique)) and unique-PPI (PPIs (Unique)) FDR control options are retained and continue to report only results for which peptides can be uniquely mapped to proteins.

New license self-service

• http://i.pfind.net:8002/license/pLink-v3.1-or-latest

pLink3 Zoom Version 3.1.4 (for Reviewers)

3.1.4 for Reviewers - 2026-03-05

New Features

• When RAW(Astral)(FAIMS) is selected for the MS Data Format, the generated .plink parameter file automatically includes search hyperparameters optimized for Astral.
• Reviewers can use the software anonymously (no registration license information required).

pLink3 Zoom version 3.1.4

3.1.4 preview - 2025-12-18

New Features

• High-performance support for data from the Thermo Scientific Orbitrap Astral and Orbitrap Astral Zoom mass spectrometers.

  • In particular, searching Astral Zoom data is 17.2–70.9× faster than pLink 3.0.

• High-performance support for searching ultra–large-scale datasets.

  • Successfully tested on a single processing that searched nearly 400 RAW files, totaling over 100 million spectra.
    • Search completed within 3 days (avg. 9.3 min per RAW file). Database: ~6k proteins. CPUs: used 48 logical processors.
    • Server configuration: 512 GB RAM and dual Intel® Xeon® Gold 6254 CPUs (2 × 18 cores; 72 logical processors total).
  • Combined FDR filtering stage time is over 4× faster compared to pLink 3.0.

• Supports for searching extremely large RAW files (a single file up to ~40 GB, extracting >3 million spectra).

Other Improvements and Fixes

• Additional optimizations and known bug fixes have been implemented.