Generated summary
PXD008990 is a DDA label-free dataset (Rattus norvegicus) with 70 runs, 70 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 534,367 PSMs, 11,095 peptidoforms and 2,195 protein groups, and the repository holds 3,558 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 534367 where the producer reported 534368 (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 534367 where the producer reported 534368 (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.
cysteine_poor warning
0.92% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
0.92% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
low_core_use warning
13.44 avg cores of 32 allowed (S5)
13.44 avg cores of 32 allowed (S5)
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 46542 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12849 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 46542 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12849 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).
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: 678 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: 678 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
10 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
10 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 | 534,367 |
| Peptidoforms at 1% FDR | 11,095 |
| Protein groups at 1% FDR | 2,195 |
| PTM sites | 3,558 |
| Quantitative values | 1,225,696 |
| PSMs, all (including decoys and sub-threshold) | 1,182,768 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 37.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
How it was measured
- Organism searched
- Rattus norvegicus (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
- 70 / 70
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0bf698d2cd0a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 755 |
| Deamidation on N | UNIMOD:7 | 587 |
| Deamidation on Q | UNIMOD:7 | 472 |
| Phosphoserine on S | UNIMOD:21 | 123 |
| Sodium on E | UNIMOD:30 | 112 |
| N-acetylalanine on A | UNIMOD:1 | 104 |
| Calcium on E | UNIMOD:951 | 101 |
| Hydroxylation on P | UNIMOD:35 | 89 |
| Calcium on D | UNIMOD:951 | 87 |
| Sodium on D | UNIMOD:30 | 83 |
| Citrullination on R | UNIMOD:7 | 79 |
| Fe[II] on E | UNIMOD:952 | 65 |
| Magnesium on E | UNIMOD:956 | 62 |
| Acetylation on X | UNIMOD:1 | 57 |
| Magnesium on D | UNIMOD:956 | 50 |
| Fe[II] on D | UNIMOD:952 | 48 |
| Carbamyl on M | UNIMOD:5 | 46 |
| N-acetylmethionine on M | UNIMOD:1 | 46 |
| N-acetylserine on S | UNIMOD:1 | 43 |
| Hydroxylation on N | UNIMOD:35 | 33 |
| Ammonia loss on N | UNIMOD:385 | 32 |
| Potassium on D | UNIMOD:530 | 27 |
| Water Loss on E | UNIMOD:27 | 25 |
| Fe[III] on E | UNIMOD:1870 | 22 |
| N6-acetyllysine on K | UNIMOD:1 | 22 |
| Phosphorylation on T | UNIMOD:21 | 20 |
| Hydroxylation on K | UNIMOD:35 | 19 |
| Potassium on E | UNIMOD:530 | 19 |
| Phosphorylation on S | UNIMOD:21 | 18 |
| Methylation on K | UNIMOD:34 | 17 |
| Phosphothreonine on T | UNIMOD:21 | 15 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 13 |
| Carbamyl on X | UNIMOD:5 | 11 |
| Carbamyl on C | UNIMOD:5 | 10 |
| Glutarylation on K | UNIMOD:1848 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 10 |
| Omega-N-methylarginine on R | UNIMOD:34 | 10 |
| Acetylation on K | UNIMOD:1 | 9 |
| 4-hydroxyproline on P | UNIMOD:35 | 8 |
| Dimethylation on K | UNIMOD:36 | 8 |
| Trimethylation on K | UNIMOD:37 | 8 |
| Methylation on R | UNIMOD:34 | 7 |
| N-myristoyl glycine on G | UNIMOD:45 | 7 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 7 |
| Nitrosylation on C | UNIMOD:275 | 7 |
| Dimethylation on R | UNIMOD:36 | 6 |
| Fe[III] on D | UNIMOD:1870 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 5 |
| N6-succinyllysine on K | — | 5 |
| Citrulline on R | UNIMOD:7 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Carboxylation on D | UNIMOD:299 | 3 |
| Phosphorylation on Y | UNIMOD:21 | 3 |
| Phosphotyrosine on Y | UNIMOD:21 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on K | UNIMOD:5 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Deamidated asparagine on N | UNIMOD:7 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| N6-methyllysine on K | UNIMOD:34 | 2 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Carboxylation on E | UNIMOD:299 | 1 |
| HexNAc on T | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| Phosphohistidine on H | UNIMOD:21 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| Sulfonation on Y | UNIMOD:40 | 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
058f4416abe7b18b, written 2026-10-29T10:37:18+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