Generated summary
PXD002467 is a DDA label-free dataset (Rattus norvegicus) with 96 runs, 48 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,453,769 PSMs, 44,050 peptidoforms and 6,747 protein groups, and the repository holds 29,726 PTM sites for it. 5 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, 5 warnings and 2 for information
count_mismatch warning
The bundle holds 1.45377e+06 where the producer reported 1.45382e+06 (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 1.45377e+06 where the producer reported 1.45382e+06 (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
9.41 avg cores of 32 allowed (S5)
9.41 avg cores of 32 allowed (S5)
occupancy_not_stored warning
Of 32580 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11348 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 32580 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11348 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: 2370 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: 2370 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), 1 row(s) dropped, e.g. PXD002467:A0ABK0LI91;Q9EQC9 written 2 times; quant_values: 48 identifier(s), 48 row(s) dropped, e.g. PXD002467:design:CYT_BO_1:protein_group:PXD002467:A0ABK0LI91;Q9EQC9: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. PXD002467:A0ABK0LI91;Q9EQC9 written 2 times; quant_values: 48 identifier(s), 48 row(s) dropped, e.g. PXD002467:design:CYT_BO_1:protein_group:PXD002467:A0ABK0LI91;Q9EQC9:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
109 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
109 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 | 1,453,769 |
| Peptidoforms at 1% FDR | 44,050 |
| Protein groups at 1% FDR | 6,747 |
| PTM sites | 29,726 |
| Quantitative values | 1,848,395 |
| PSMs, all (including decoys and sub-threshold) | 7,073,531 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 38.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.8% |
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
- 96 / 48
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- fbfc3c110165
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 20,041 |
| Oxidation on M | UNIMOD:35 | 6,679 |
| Phosphoserine on S | UNIMOD:21 | 1,177 |
| Phosphothreonine on T | UNIMOD:21 | 228 |
| N-acetylalanine on A | UNIMOD:1 | 195 |
| Hydroxylation on P | UNIMOD:35 | 134 |
| N6-acetyllysine on K | UNIMOD:1 | 117 |
| N-acetylmethionine on M | UNIMOD:1 | 106 |
| N-acetylserine on S | UNIMOD:1 | 85 |
| 4-hydroxyproline on P | UNIMOD:35 | 80 |
| Acetylation on X | UNIMOD:1 | 76 |
| Omega-N-methylarginine on R | UNIMOD:34 | 63 |
| Phosphotyrosine on Y | UNIMOD:21 | 48 |
| N6-succinyllysine on K | — | 38 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 27 |
| Phosphorylation on S | UNIMOD:21 | 24 |
| N6-glutaryllysine on K | — | 22 |
| Methylation on K | UNIMOD:34 | 21 |
| Phosphorylation on T | UNIMOD:21 | 20 |
| Hydroxylation on K | UNIMOD:35 | 17 |
| Deamidated asparagine on N | UNIMOD:7 | 16 |
| N-acetylthreonine on T | UNIMOD:1 | 15 |
| Acetylation on K | UNIMOD:1 | 14 |
| Methylation on R | UNIMOD:34 | 11 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 11 |
| Allysine on K | UNIMOD:352 | 10 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 10 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Dimethylation on R | UNIMOD:36 | 8 |
| HexNAc on S | UNIMOD:43 | 8 |
| HexNAc on T | UNIMOD:43 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| N-myristoyl glycine on G | UNIMOD:45 | 7 |
| Hydroxyproline on P | UNIMOD:35 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| Citrulline on R | UNIMOD:7 | 5 |
| Dimethylation on K | UNIMOD:36 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| Trimethylation on K | UNIMOD:37 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| N6-lipoyllysine on K | UNIMOD:42 | 3 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylproline on P | UNIMOD:1 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 2 |
| (3R)-3-hydroxyaspartate on D | UNIMOD:35 | 1 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(pyridoxal phosphate)lysine on K | UNIMOD:46 | 1 |
| N6-methacryllysine on K | — | 1 |
| Pros-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Sulfocysteine on C | UNIMOD:40 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
48508b7393e3ae36, written 2026-10-29T09:43:45+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