Generated summary
PXD049018 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 104,625 PSMs, 17,575 peptidoforms and 1,626 protein groups, and the repository holds 10,007 PTM sites for it. 6 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, 6 warnings and 1 for information
count_mismatch warning
The bundle holds 104625 where the producer reported 104634 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 104625 where the producer reported 104634 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
high_contamination warning
45.52% of protein intensity in the worst file, 5.10% median across 20 files (DEF-QC-9 v3.5)
45.52% of protein intensity in the worst file, 5.10% median across 20 files (DEF-QC-9 v3.5)
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.
occupancy_not_stored warning
Of 16669 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1123 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
Of 16669 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1123 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).
spectral_library warning
human's current library moved from version 74 to 75 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD049018\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-08-13-49.msp and has NOT been registered, so nothing was lost; merge it deliberately.
human's current library moved from version 74 to 75 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD049018\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-08-13-49.msp and has NOT been registered, so nothing was lost; merge it deliberately.
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: 152 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: 152 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.
occupancy_decoy_groups info
21 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
21 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 | 104,625 |
| Peptidoforms at 1% FDR | 17,575 |
| Protein groups at 1% FDR | 1,626 |
| PTM sites | 10,007 |
| Quantitative values | 129,175 |
| PSMs, all (including decoys and sub-threshold) | 400,599 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 17.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 10.9% |
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
- proximity_labelling
- Instrument vendor
- not recorded
- Runs / samples
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 2,929 |
| Carbamidomethyl on C | UNIMOD:4 | 2,272 |
| Deamidation on Q | UNIMOD:7 | 665 |
| Hydroxylation on P | UNIMOD:35 | 605 |
| Deamidation on N | UNIMOD:7 | 564 |
| Hydroxylation on K | UNIMOD:35 | 256 |
| Hydroxylation on N | UNIMOD:35 | 224 |
| Ammonia loss on N | UNIMOD:385 | 179 |
| Citrullination on R | UNIMOD:7 | 137 |
| N-acetylalanine on A | UNIMOD:1 | 127 |
| Phosphoserine on S | UNIMOD:21 | 99 |
| Calcium on E | UNIMOD:951 | 82 |
| Fe[III] on D | UNIMOD:1870 | 80 |
| Fe[III] on E | UNIMOD:1870 | 77 |
| Methylation on K | UNIMOD:34 | 72 |
| Carbamyl on X | UNIMOD:5 | 71 |
| Magnesium on E | UNIMOD:956 | 67 |
| Acetylation on K | UNIMOD:1 | 65 |
| Magnesium on D | UNIMOD:956 | 65 |
| Ammonia loss on C | UNIMOD:385 | 63 |
| Sodium on E | UNIMOD:30 | 63 |
| Calcium on D | UNIMOD:951 | 54 |
| Carbamyl on M | UNIMOD:5 | 51 |
| Water Loss on E | UNIMOD:27 | 49 |
| Sodium on D | UNIMOD:30 | 48 |
| N-acetylmethionine on M | UNIMOD:1 | 46 |
| Phosphorylation on S | UNIMOD:21 | 46 |
| N6-acetyllysine on K | UNIMOD:1 | 45 |
| Formylation on K | UNIMOD:122 | 38 |
| N-acetylserine on S | UNIMOD:1 | 36 |
| 4-hydroxyproline on P | UNIMOD:35 | 35 |
| Dimethylation on K | UNIMOD:36 | 32 |
| Fe[II] on E | UNIMOD:952 | 32 |
| Phosphorylation on T | UNIMOD:21 | 32 |
| Fe[II] on D | UNIMOD:952 | 30 |
| Methylation on R | UNIMOD:34 | 28 |
| Potassium on E | UNIMOD:530 | 27 |
| Acetylation on X | UNIMOD:1 | 21 |
| Phosphothreonine on T | UNIMOD:21 | 20 |
| N6-methyllysine on K | UNIMOD:34 | 19 |
| Cu[I] on D | UNIMOD:531 | 18 |
| Dimethylation on R | UNIMOD:36 | 18 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 18 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 18 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 15 |
| Carboxylation on E | UNIMOD:299 | 14 |
| Deamidated asparagine on N | UNIMOD:7 | 14 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| Potassium on D | UNIMOD:530 | 12 |
| Malonylation on K | UNIMOD:747 | 11 |
| Phosphorylation on Y | UNIMOD:21 | 11 |
| Carboxylation on D | UNIMOD:299 | 9 |
| Hydroxybutyrylation on K | — | 9 |
| Sulfonation on Y | UNIMOD:40 | 9 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 8 |
| Butyrylation on K | UNIMOD:1289 | 8 |
| HexNAc on S | UNIMOD:43 | 7 |
| Trimethylation on K | UNIMOD:37 | 7 |
| Zinc on D | UNIMOD:954 | 7 |
| Glutarylation on K | UNIMOD:1848 | 6 |
| Carbamyl on K | UNIMOD:5 | 5 |
| Cu[I] on E | UNIMOD:531 | 5 |
| N6-glutaryllysine on K | — | 5 |
| Omega-N-methylarginine on R | UNIMOD:34 | 5 |
| HexNAc on T | UNIMOD:43 | 4 |
| Nitrosylation on Y | UNIMOD:354 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carbamyl on R | UNIMOD:5 | 3 |
| N6-methacryllysine on K | — | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Carboxylation on K | UNIMOD:299 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N6-succinyllysine on K | — | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Pyridoxal phosphate on K | UNIMOD:46 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| Succinylation on K | UNIMOD:64 | 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
1feb470e25d0ea89, written 2026-10-29T09:20:18+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