Generated summary
PXD058253 is a DDA label-free dataset (Rattus norvegicus) with 38 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 12,726 PSMs, 234 peptidoforms and 139 protein groups, and the repository holds 1,541 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 12726 where the producer reported 12736 (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 12726 where the producer reported 12736 (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.
low_core_use warning
14.83 avg cores of 32 allowed (S5)
14.83 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 12736/524985 = 2.43% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 12736/524985 = 2.43% of MS2 identified (S3)
occupancy_not_stored warning
Of 6846 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 78 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 6846 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 78 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_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 131 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: 131 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
57 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
57 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 | 12,726 |
| Peptidoforms at 1% FDR | 234 |
| Protein groups at 1% FDR | 139 |
| PTM sites | 1,541 |
| Quantitative values | 23,525 |
| PSMs, all (including decoys and sub-threshold) | 395,189 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 2.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 72.6% |
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
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 38 / 19
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 195 |
| Nethylmaleimide on C | UNIMOD:108 | 66 |
| Glutarylation on K | UNIMOD:1848 | 57 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 53 |
| Deamidation on N | UNIMOD:7 | 51 |
| Deamidation on Q | UNIMOD:7 | 44 |
| Hydroxylation on P | UNIMOD:35 | 40 |
| Citrullination on R | UNIMOD:7 | 30 |
| Hydroxylation on N | UNIMOD:35 | 23 |
| Hydroxylation on K | UNIMOD:35 | 19 |
| Ammonia loss on N | UNIMOD:385 | 15 |
| Phosphoserine on S | UNIMOD:21 | 13 |
| Phosphorylation on S | UNIMOD:21 | 10 |
| Formylation on K | UNIMOD:122 | 9 |
| Magnesium on E | UNIMOD:956 | 8 |
| Calcium on E | UNIMOD:951 | 7 |
| Methylation on K | UNIMOD:34 | 7 |
| Dimethylation on R | UNIMOD:36 | 6 |
| Methylation on R | UNIMOD:34 | 6 |
| Sodium on D | UNIMOD:30 | 6 |
| Dimethylation on K | UNIMOD:36 | 5 |
| Magnesium on D | UNIMOD:956 | 5 |
| N-acetylalanine on A | UNIMOD:1 | 5 |
| N6-acetyllysine on K | UNIMOD:1 | 5 |
| HexNAc on S | UNIMOD:43 | 4 |
| HexNAc on T | UNIMOD:43 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| Acetylation on K | UNIMOD:1 | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| Phosphorylation on Y | UNIMOD:21 | 3 |
| Sodium on E | UNIMOD:30 | 3 |
| Water Loss on E | UNIMOD:27 | 3 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Calcium on D | UNIMOD:951 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| Deamidated asparagine on N | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6-succinyllysine on K | — | 2 |
| Omega-N-methylarginine on R | UNIMOD:34 | 2 |
| Phosphothreonine on T | UNIMOD:21 | 2 |
| Potassium on E | UNIMOD:530 | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| Carboxylation on D | UNIMOD:299 | 1 |
| Cu[I] on E | UNIMOD:531 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylmethionine on M | UNIMOD:1 | 1 |
| Nitrosylation on Y | UNIMOD:354 | 1 |
| Phosphorylation on T | UNIMOD:21 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Potassium on D | UNIMOD:530 | 1 |
| Pyridoxal phosphate on K | UNIMOD:46 | 1 |
| Sulfonation on Y | UNIMOD:40 | 1 |
| Zinc on E | UNIMOD:954 | 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
18e54e88b81662d8, written 2026-10-29T09:13:43+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