Derived data, analysis code and search exports for a controlled re-analysis of peptide-evidence restriction, aggregation order and match-between-runs in ECM proteomics

This record contains the derived data, analysis code and search exports produced by a controlled re-analysis of publicly available mass-spectrometry proteomics datasets on the extracellular matrix (ECM) and the matrisome. It accompanies a manuscript that tests how peptide-evidence restriction, protein-aggregation order and match-between-runs handling change protein-level contrasts. Contents Analysis_Data_and_Code.zip — per-dataset derived tables (protein- and peptide-level results, design and contrast plans), the analysis code and configuration, provenance records and reproduction checks. Search_Outputs_and_Reference.zip — search-engine outputs and parameters, the reference FASTA, workflow exports and the search-export file manifest. README_dataset.md — description of both archives and of the scope limits stated below. SHA256SUMS.txt — SHA256 checksums of the two archives. Scope limits No raw mass-spectrometry spectra are redistributed in this record. The raw data and their metadata belong to the original studies and remain available from their own repositories (see Related identifiers): jPOST JPST003540 (ProteomeXchange PXD060346) and jPOST JPST003579 (PXD060345), together with PRIDE PXD040684, PXD025842 and PXD066357. The DOI of this record identifies the derived tables and code only. It does not replace, mirror or extend any raw-data accession, and it must not be cited as the source of the raw spectra. Integrity File sizes and SHA256 digests are listed in SHA256SUMS.txt and README_dataset.md. Released under CC BY 4.0.