Generated summary
PXD018969 is a DDA label-free dataset (Homo sapiens) with 19 runs, 19 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 220,119 PSMs, 17,592 peptidoforms and 2,966 protein groups, and the repository holds 4,903 PTM sites for it. 7 open warnings about it are recorded.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.
Open findings
Recorded against this dataset: 0 errors, 7 warnings and 3 for information
contaminant_label_unresolved warning
12 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: O76009, O76011, O76013, O76014, O76015.
12 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: O76009, O76011, O76013, O76014, O76015.
count_mismatch warning
The bundle holds 220119 where the producer reported 220121 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 220119 where the producer reported 220121 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
high_contamination warning
26.15% of protein intensity in the worst file, 5.19% median across 19 files (DEF-QC-9 v3.5)
26.15% of protein intensity in the worst file, 5.19% median across 19 files (DEF-QC-9 v3.5)
no_design_file warning
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
no_sdrf warning
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.
unplaced_ptm_sites warning
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 128 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 128 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
upstream_provenance_changed warning
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD018969/02_fetch/provenance.json) with sha256 ecb4d638b7f56f6771e60d071be6abb33ac55ca981fa38f5814bd423ff2db9b4, and the file there now has 9e7b142dfe582c4bbdfa4f3d863922adbf2efd5fac6fda48bfc8d1a524e980c9: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the fetch stage is gone unless the producer archived it.
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD018969/02_fetch/provenance.json) with sha256 ecb4d638b7f56f6771e60d071be6abb33ac55ca981fa38f5814bd423ff2db9b4, and the file there now has 9e7b142dfe582c4bbdfa4f3d863922adbf2efd5fac6fda48bfc8d1a524e980c9: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the fetch stage is gone unless the producer archived it.
collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD018969:P49916;P49916-3 written 2 times; quant_values: 19 identifier(s), 19 row(s) dropped, e.g. PXD018969:812042892gro_Mocksoluble1:label_free:protein_group:PXD018969:P49916;P49916-3:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD018969:P49916;P49916-3 written 2 times; quant_values: 19 identifier(s), 19 row(s) dropped, e.g. PXD018969:812042892gro_Mocksoluble1:label_free:protein_group:PXD018969:P49916;P49916-3:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
no_output_sdrf info
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
occupancy_decoy_groups info
28 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
28 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
What was found
| PSMs at 1% FDR | 220,119 |
| Peptidoforms at 1% FDR | 17,592 |
| Protein groups at 1% FDR | 2,966 |
| PTM sites | 4,903 |
| Quantitative values | 207,369 |
| PSMs, all (including decoys and sub-threshold) | 808,940 |
| MS2 identification rate (aging:DEF-ID-RATE) | 31.3% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 6.5% |
How it was measured
- Organism searched
- Homo sapiens (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- none
- Instrument vendor
- not recorded
- Runs / samples
- 19 / 19
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000005640_AND_revi_2026_09_18_agingPTM-v1.xml
- Pipeline commit
- 19dd466d103f
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Deamidation on N | UNIMOD:7 | 1,385 |
| Deamidation on Q | UNIMOD:7 | 983 |
| Oxidation on M | UNIMOD:35 | 578 |
| N-acetylalanine on A | UNIMOD:1 | 173 |
| Ammonia loss on N | UNIMOD:385 | 153 |
| Phosphoserine on S | UNIMOD:21 | 131 |
| Citrullination on R | UNIMOD:7 | 118 |
| Carbamidomethyl on C | UNIMOD:4 | 109 |
| Hydroxylation on P | UNIMOD:35 | 96 |
| N-acetylmethionine on M | UNIMOD:1 | 86 |
| Sodium on E | UNIMOD:30 | 70 |
| Carbamyl on X | UNIMOD:5 | 69 |
| N-acetylserine on S | UNIMOD:1 | 59 |
| Magnesium on E | UNIMOD:956 | 56 |
| Hydroxylation on N | UNIMOD:35 | 39 |
| Sodium on D | UNIMOD:30 | 39 |
| Water Loss on E | UNIMOD:27 | 34 |
| Acetylation on X | UNIMOD:1 | 32 |
| N6-acetyllysine on K | UNIMOD:1 | 31 |
| Magnesium on D | UNIMOD:956 | 27 |
| Phosphorylation on S | UNIMOD:21 | 24 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 22 |
| Dimethylation on K | UNIMOD:36 | 22 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 22 |
| Methylation on K | UNIMOD:34 | 20 |
| Calcium on E | UNIMOD:951 | 18 |
| N6-methyllysine on K | UNIMOD:34 | 18 |
| 4-hydroxyproline on P | UNIMOD:35 | 17 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| Phosphorylation on T | UNIMOD:21 | 15 |
| Hydroxylation on K | UNIMOD:35 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 11 |
| Formylation on K | UNIMOD:122 | 11 |
| N-acetylthreonine on T | UNIMOD:1 | 10 |
| Carboxylation on E | UNIMOD:299 | 9 |
| Omega-N-methylarginine on R | UNIMOD:34 | 9 |
| Dimethylation on R | UNIMOD:36 | 8 |
| HexNAc on T | UNIMOD:43 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 8 |
| Calcium on D | UNIMOD:951 | 7 |
| HexNAc on S | UNIMOD:43 | 7 |
| Methylation on R | UNIMOD:34 | 7 |
| Acetylation on K | UNIMOD:1 | 6 |
| N6-succinyllysine on K | — | 6 |
| Potassium on E | UNIMOD:530 | 6 |
| Carboxylation on K | UNIMOD:299 | 5 |
| Nitrosylation on C | UNIMOD:275 | 5 |
| Sulfonation on Y | UNIMOD:40 | 5 |
| Butyrylation on K | UNIMOD:1289 | 4 |
| Carbamyl on K | UNIMOD:5 | 4 |
| Carbamyl on R | UNIMOD:5 | 4 |
| Carboxylation on D | UNIMOD:299 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-myristoyl glycine on G | UNIMOD:45 | 4 |
| Phosphothreonine on T | UNIMOD:21 | 4 |
| Carbamyl on M | UNIMOD:5 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-crotonyllysine on K | — | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| Phosphorylation on Y | UNIMOD:21 | 2 |
| Phosphotyrosine on Y | UNIMOD:21 | 2 |
| Potassium on D | UNIMOD:530 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Trimethylation on K | UNIMOD:37 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-methacryllysine on K | — | 1 |
| O-(pantetheine 4'-phosphoryl)serine on S | UNIMOD:49 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Tele-methylhistidine on H | UNIMOD:34 | 1 |
Every modification with a site on a target protein, most frequent first. A dash in the UNIMOD
column means the modification has no UNIMOD term in the registry that searched it, not that it is
unknown. One chemistry can appear under two names (UniProt's and MetaMorpheus's); the catalog's
ptm_sites_by_chemistry view merges them.
Data
The Parquet files for this dataset are not published yet.
- Bundle
192fd7e3153006bb, written 2026-10-29T10:59:10+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group