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Proteomics changelog

1.2.0​

  • Shared enrichment charts now survive reopen — a published/shared analysis's enrichment dot and bar charts no longer lose their value column (the "Column negLog10FDR does not exist" error) when the project is reopened, and the Up/Down term tables no longer leak into the project as extra tables. The charts are now self-contained on the enrichment frame and split by direction via a per-viewer filter.
  • Volcano opens automatically on Candidates import — importing a Spectronaut Candidates file now lands you on the volcano immediately, matching the Report → Differential Expression path (Candidates arrive with the result already computed, so the pipeline's DE step is skipped).
  • Personas & capabilities documentation — a reference describing what the proteomics analyst vs. the biology scientist can do and how that boundary is enforced.

0.2.0​

  • Organism-aware subcellular-location coloring — the volcano's "color by subcellular location" now fetches UniProt annotations for the experiment's organism (persisted as a proteomics.organism tag from the Enrichment dialog), so non-human data is no longer mis-colored by human entries. The taxonomy filter applies only to the reviewed-by-gene fallback; accession lookups stay unfiltered, and all 9 supported organisms are covered.
  • Internal consistency — significance thresholds, the direction palette, and column-name constants are now single-sourced instead of duplicated across files; the differential- expression FDR cutoff is wired through to the BH correction.
  • README — illustrated with the main analysis view, an authored pipeline diagram, and an enrichment→volcano cross-link walkthrough.

0.1.0​

Initial release — mass spectrometry-based proteomics analysis, carrying a study from search-engine output to biological interpretation inside Datagrok.

  • Import — MaxQuant (proteinGroups.txt), Spectronaut Report (PG-level, including streaming aggregation of long-form precursor exports), Spectronaut Candidates (pre-computed differential expression), FragPipe (combined_protein.tsv), and a generic CSV/TSV column-mapping importer. Contaminant/decoy filtering, log2 transformation, and semantic-type tagging are applied on import.
  • Pipeline — experiment annotation (group assignment), normalization (median / quantile / VSN), missing-value imputation (kNN / MinProb / mean / median / zero), and differential expression cascading DEqMS → limma → client-side Welch's t-test.
  • Visualization — volcano, clustered expression heatmap, sample-level PCA, group-mean correlation, QC dashboard (MA / CV / missingness / intensity trend), and an SPC dashboard with Nelson-rule instrument monitoring.
  • Biological interpretation — g:Profiler over-representation analysis (GO, KEGG, Reactome, WikiPathways across 9 organisms) with dot/bar charts cross-linked to the volcano, plus a UniProt context panel for per-protein metadata.
  • Sharing — publish read-only, access-verified, versioned review snapshots (table + volcano + enrichment) to a reviewer group.
  • R scripts (limma, DEqMS, VSN) run server-side with client-side fallbacks throughout, so the package is fully functional without a configured R environment.