Add 189 automated E. coli SDRF annotations (batch 3: multi-organism + PTM-recovered)

[ypriverol]

E. coli SDRF annotations — automated batch 3 (189 datasets)

189 further Escherichia coli ProteomeXchange datasets, recovered by an upgraded
annotation pipeline. Includes 142 multi-organism datasets (organism assigned
per sample from the set PRIDE declares for the project) and 47 single-organism
datasets newly recovered after fixing modification formatting.

Pipeline (same base as batches 1-2, plus):

• Structured modifications: compact PTM descriptions are split into separate
  comment[modification parameters] columns, each mapped to canonical UNIMOD
  (NT=<name>;AC=UNIMOD:<id>;TA=<residue>;MT=<Fixed|Variable>); unknown mods dropped.
• Organism: plain NCBITaxon name; for single-organism projects grounded to
  PRIDE's declaration; for multi-organism projects verified to be one of the
  declared organisms (out-of-set assignments excluded from this batch).
• comment[sdrf template] recorded; CV accessions resolved against PSI-MS/UNIMOD.
• All files pass parse_sdrf validate-sdrf -t ms-proteomics.

First-pass automated annotations — review welcome. Empirical instrument / mass
tolerance / modification verification from the raw spectra is a planned follow-up.

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Important

Review skipped

Review was skipped due to path filters

⛔ Files ignored due to path filters (189)

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