Generated summary
PXD059818 is a DDA label-free dataset (Mus musculus) with 38 runs, 38 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 505,085 PSMs, 38,626 peptidoforms and 4,439 protein groups, and the repository holds 20,174 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 2 for information
count_mismatch warning
The bundle holds 505085 where the producer reported 505109 (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 505085 where the producer reported 505109 (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
48.80% of protein intensity in the worst file, 5.29% median across 38 files (DEF-QC-9 v3.5)
48.80% of protein intensity in the worst file, 5.29% median across 38 files (DEF-QC-9 v3.5)
low_core_use warning
15.08 avg cores of 32 allowed (S5)
15.08 avg cores of 32 allowed (S5)
occupancy_not_stored warning
Of 68136 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7288 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 68136 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7288 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).
sdrf_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: cell type: astrocyte, excitatory neuron, immature microglia; organism part: BV2 cell, brain cortex. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: cell type: astrocyte, excitatory neuron, immature microglia; organism part: BV2 cell, brain cortex. Match on it as text; it has not been mapped to a term.
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: 1850 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: 1850 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.
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), 2 row(s) dropped, e.g. PXD059818:O88207;Q61245;Q64739 written 3 times; quant_values: 38 identifier(s), 76 row(s) dropped, e.g. PXD059818:christina_Aldh1l1_Camk2a_21ip_01:label_free:protein_group:PXD059818:O88207;Q61245;Q64739:QuantProject:DEF-PROT-SPC written 3 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), 2 row(s) dropped, e.g. PXD059818:O88207;Q61245;Q64739 written 3 times; quant_values: 38 identifier(s), 76 row(s) dropped, e.g. PXD059818:christina_Aldh1l1_Camk2a_21ip_01:label_free:protein_group:PXD059818:O88207;Q61245;Q64739:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
46 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
46 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 | 505,085 |
| Peptidoforms at 1% FDR | 38,626 |
| Protein groups at 1% FDR | 4,439 |
| PTM sites | 20,174 |
| Quantitative values | 836,295 |
| PSMs, all (including decoys and sub-threshold) | 908,125 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 33.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 6.2% |
How it was measured
- Organism searched
- Mus musculus (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- proximity_labelling
- Instrument vendor
- Thermo
- Runs / samples
- 38 / 38
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0ba5e4c3fd33
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 7,996 |
| Oxidation on M | UNIMOD:35 | 3,721 |
| Deamidation on N | UNIMOD:7 | 1,835 |
| Deamidation on Q | UNIMOD:7 | 611 |
| Hydroxylation on P | UNIMOD:35 | 444 |
| Sodium on E | UNIMOD:30 | 412 |
| Sodium on D | UNIMOD:30 | 373 |
| Phosphoserine on S | UNIMOD:21 | 322 |
| Hydroxylation on N | UNIMOD:35 | 241 |
| N-acetylalanine on A | UNIMOD:1 | 213 |
| Ammonia loss on N | UNIMOD:385 | 206 |
| Citrullination on R | UNIMOD:7 | 190 |
| Calcium on E | UNIMOD:951 | 176 |
| Calcium on D | UNIMOD:951 | 156 |
| Ammonia loss on C | UNIMOD:385 | 147 |
| Acetylation on X | UNIMOD:1 | 127 |
| Fe[III] on E | UNIMOD:1870 | 122 |
| Fe[III] on D | UNIMOD:1870 | 115 |
| Carbamyl on X | UNIMOD:5 | 107 |
| Phosphorylation on S | UNIMOD:21 | 104 |
| Carbamyl on M | UNIMOD:5 | 93 |
| N-acetylmethionine on M | UNIMOD:1 | 85 |
| N-acetylserine on S | UNIMOD:1 | 82 |
| Phosphorylation on T | UNIMOD:21 | 73 |
| Phosphothreonine on T | UNIMOD:21 | 63 |
| Magnesium on D | UNIMOD:956 | 61 |
| Magnesium on E | UNIMOD:956 | 60 |
| Hydroxylation on K | UNIMOD:35 | 57 |
| Water Loss on E | UNIMOD:27 | 52 |
| Methylation on K | UNIMOD:34 | 47 |
| N6-acetyllysine on K | UNIMOD:1 | 41 |
| Fe[II] on E | UNIMOD:952 | 33 |
| Methylation on R | UNIMOD:34 | 32 |
| Carbamyl on K | UNIMOD:5 | 27 |
| Acetylation on K | UNIMOD:1 | 25 |
| Fe[II] on D | UNIMOD:952 | 24 |
| HexNAc on T | UNIMOD:43 | 24 |
| Potassium on E | UNIMOD:530 | 24 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 23 |
| N-acetylthreonine on T | UNIMOD:1 | 22 |
| Dimethylation on R | UNIMOD:36 | 19 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 16 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| Omega-N-methylarginine on R | UNIMOD:34 | 16 |
| HexNAc on S | UNIMOD:43 | 15 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| Phosphorylation on Y | UNIMOD:21 | 12 |
| Formylation on K | UNIMOD:122 | 11 |
| Dimethylation on K | UNIMOD:36 | 10 |
| N6-methyllysine on K | UNIMOD:34 | 10 |
| N6-succinyllysine on K | — | 10 |
| Phosphotyrosine on Y | UNIMOD:21 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| Potassium on D | UNIMOD:530 | 7 |
| 4-hydroxyproline on P | UNIMOD:35 | 5 |
| Butyrylation on K | UNIMOD:1289 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| Carboxylation on D | UNIMOD:299 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| Hydroxybutyrylation on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Trimethylation on K | UNIMOD:37 | 4 |
| Carbamyl on C | UNIMOD:5 | 3 |
| Carboxylation on E | UNIMOD:299 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-glutaryllysine on K | — | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| N6-crotonyllysine on K | — | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Carboxylation on K | UNIMOD:299 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
7cabc1fa3f59a154, written 2026-10-29T10:49:10+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