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ProSE: rescore all runs of a multi-file search with one joint Percolator model

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#10,581 4 bình luận 0 reaction 0 người được giao Xem trên GitHub

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@satyam102006 đang làm issue này rồi.

Từ ngày 15/10/2026.

Đánh giá

Độ khó
5/5
Thời gian dự kiến
Hơn một tuần
Mức phù hợp với người mới
8/100
Loại issue
Tính năng
Độ rõ ràng
Khá rõ ràng
Mức độ hoạt động
Sôi nổi
Công nghệ
cpp
Lĩnh vực
data

Hướng nghiên cứu

The per-file rescoring lives in ProSEAlgorithm::applyPsmFDR_, called from the multi-file loop in searchWithModificationAnalysis(), and Percolator::rescorePSMs trains and scores one list at a time. Read how MultiFileSearchResult::per_file holds the PSMs, then decide how training across all runs fits before per-run scoring. Done means the two-file, blank-like and per_run tests described in the issue pass.

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Mô tả

Motivation

With #10578, ProSE rescores PSMs with Percolator by default (Search:rescore). Each input file is rescored on its own and gets its own model. Small runs suffer from this:

  • Single-cell runs and other small runs: each run trains a model on its own few PSMs. A run with fewer than 100 PSMs, or without decoy PSMs, is not rescored at all and keeps its HyperScore-based q-values. A run just above that limit gets a model trained on very little data. The 100 PSMs are all PSMs (best hit per spectrum, targets and decoys, before the FDR filter), not confident identifications.
  • Blanks: a blank easily has more than 100 PSMs, all of them false. Percolator then runs. Its sanity check finds no targets at q < test FDR and falls back to the best single feature (Resetting score vector, using default vector). The result is conservative: in a simulation with real spectra against a random database, 0 target PSMs passed 5% FDR. But the run is reported as rescored.
  • Batches with -out_merged: if Percolator rescores only some files (e.g. one blank or one small run in a batch), the runs report different search engines and scores. They cannot be pooled, so -out_merged fails (since #10578 with exit code INCOMPATIBLE_INPUT_DATA). With rescoring on by default, this hits typical single-cell batches.

Proposal

For multi-file searches, train one Percolator model on the PSMs of all runs (a joint model, as mokapot offers for single-cell data). Apply it to every run, and compute q-values per run (and on the pooled set for -out_merged).

  • Small runs and blanks are scored with a model trained on enough data. Only the q-value estimate stays per run.
  • All runs carry Percolator scores, so -out_merged always works. The mixed outcome disappears, except when the whole batch has too few PSMs or no decoys.
  • Keep per-run models as an option, e.g. a parameter rescore:model with joint (default for more than one file) and per_run.

Implementation notes

  • Today the rescoring sits in ProSEAlgorithm::applyPsmFDR_, which the multi-file path of searchWithModificationAnalysis() calls per file inside its search loop. A joint model needs the PSMs of all files first: train after all searches, then apply the model and the PSM FDR per file, then compute the run statistics, the modification analysis and the pooled aggregate.
  • Percolator::rescorePSMs trains and scores one PeptideIdentificationList. A joint model needs either one call on the concatenated PSMs, with per-run TDC and q-values afterwards from the SVM score, or a split into train (all runs) and score (each run).
  • The PIN feature set must be the same for all runs: standard features with the charge range over all runs, plus extra_features, which already match across runs of one search.
  • Memory: the PSMs of all files are kept anyway (MultiFileSearchResult::per_file), so training needs no additional copy beyond Percolator's own feature matrix.
  • The chunked multi-file loop and the distributed (sharded) workflow keep per-run models, or document that a joint model needs all shards in one process.

Also worth doing

  • Report the sanity-check fallback (learned model replaced by the best single feature) per run, instead of only the raw Resetting score vector … Use --override flag line on stderr. The flag does not exist in ProSE. This is a small change and goes into #10578.

Tests

  • A two-file search with one run below 100 PSMs: both runs get Percolator q-values, and -out_merged is written.
  • A blank-like run (real spectra, random database) in a batch: no target passes the FDR threshold, and the batch still merges.
  • per_run reproduces the current results.
Ngôn ngữ chính
C++
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Merge trung bình
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Pull request đã merge (30 ngày)
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