Generated summary
PXD026608 is a DDA label-free dataset (Rattus norvegicus) with 12 runs, 12 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 266,155 PSMs, 11,560 peptidoforms and 2,467 protein groups, and the repository holds 14,322 PTM sites for it. 4 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, 4 warnings and 2 for information
count_mismatch warning
The bundle holds 266155 where the producer reported 266219 (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 266155 where the producer reported 266219 (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.
occupancy_not_stored warning
Of 94965 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6 duplicate entry for one site and run (identical values; same protein group); 1154 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 94965 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6 duplicate entry for one site and run (identical values; same protein group); 1154 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: organism part: heart. 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: organism part: heart. 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: 1280 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: 1280 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. PXD026608:A0A0G2K8T1;A0A8I6AEA2;F1LNZ3 written 3 times; quant_values: 12 identifier(s), 24 row(s) dropped, e.g. PXD026608:HFX3_FPEP191624581-2A:label_free:protein_group:PXD026608:A0A0G2K8T1;A0A8I6AEA2;F1LNZ3: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. PXD026608:A0A0G2K8T1;A0A8I6AEA2;F1LNZ3 written 3 times; quant_values: 12 identifier(s), 24 row(s) dropped, e.g. PXD026608:HFX3_FPEP191624581-2A:label_free:protein_group:PXD026608:A0A0G2K8T1;A0A8I6AEA2;F1LNZ3:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
300 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
300 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 | 266,155 |
| Peptidoforms at 1% FDR | 11,560 |
| Protein groups at 1% FDR | 2,467 |
| PTM sites | 14,322 |
| Quantitative values | 116,616 |
| PSMs, all (including decoys and sub-threshold) | 712,605 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 28.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.4% |
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
- phospho
- Instrument vendor
- Thermo
- Runs / samples
- 12 / 12
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0ba5e4c3fd33
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Phosphorylation on S | UNIMOD:21 | 5,348 |
| Phosphorylation on T | UNIMOD:21 | 1,699 |
| Phosphoserine on S | UNIMOD:21 | 1,663 |
| Carbamidomethyl on C | UNIMOD:4 | 1,327 |
| Oxidation on M | UNIMOD:35 | 911 |
| Carbamyl on X | UNIMOD:5 | 428 |
| Formylation on K | UNIMOD:122 | 369 |
| Phosphorylation on Y | UNIMOD:21 | 310 |
| Phosphothreonine on T | UNIMOD:21 | 252 |
| Sodium on E | UNIMOD:30 | 227 |
| Sulfonation on Y | UNIMOD:40 | 168 |
| Sodium on D | UNIMOD:30 | 161 |
| Deamidation on N | UNIMOD:7 | 154 |
| Deamidation on Q | UNIMOD:7 | 130 |
| Hydroxylation on P | UNIMOD:35 | 100 |
| Magnesium on E | UNIMOD:956 | 74 |
| Ammonia loss on N | UNIMOD:385 | 73 |
| Fe[III] on E | UNIMOD:1870 | 69 |
| Fe[III] on D | UNIMOD:1870 | 62 |
| Ammonia loss on C | UNIMOD:385 | 57 |
| Magnesium on D | UNIMOD:956 | 55 |
| Water Loss on E | UNIMOD:27 | 47 |
| Phosphotyrosine on Y | UNIMOD:21 | 43 |
| N-acetylalanine on A | UNIMOD:1 | 41 |
| Carbamyl on M | UNIMOD:5 | 38 |
| Hydroxylation on N | UNIMOD:35 | 35 |
| Citrullination on R | UNIMOD:7 | 33 |
| N-acetylserine on S | UNIMOD:1 | 31 |
| Fe[II] on D | UNIMOD:952 | 23 |
| Carbamyl on K | UNIMOD:5 | 22 |
| Fe[II] on E | UNIMOD:952 | 22 |
| Acetylation on X | UNIMOD:1 | 21 |
| 4-hydroxyproline on P | UNIMOD:35 | 20 |
| Calcium on E | UNIMOD:951 | 20 |
| Calcium on D | UNIMOD:951 | 19 |
| Carboxylation on D | UNIMOD:299 | 11 |
| Potassium on E | UNIMOD:530 | 11 |
| Carboxylation on E | UNIMOD:299 | 10 |
| Cu[I] on E | UNIMOD:531 | 10 |
| Methylation on K | UNIMOD:34 | 10 |
| ADP-ribosylation on S | UNIMOD:213 | 9 |
| Nitrosylation on Y | UNIMOD:354 | 9 |
| Omega-N-methylarginine on R | UNIMOD:34 | 9 |
| Acetylation on K | UNIMOD:1 | 8 |
| Dimethylation on K | UNIMOD:36 | 8 |
| Methylation on R | UNIMOD:34 | 8 |
| Potassium on D | UNIMOD:530 | 8 |
| Carbamyl on R | UNIMOD:5 | 7 |
| Deamidated asparagine on N | UNIMOD:7 | 7 |
| N-acetylmethionine on M | UNIMOD:1 | 7 |
| Zinc on E | UNIMOD:954 | 7 |
| Cu[I] on D | UNIMOD:531 | 5 |
| Hydroxylation on K | UNIMOD:35 | 5 |
| Dimethylation on R | UNIMOD:36 | 4 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-acetylthreonine on T | UNIMOD:1 | 4 |
| N6-acetyllysine on K | UNIMOD:1 | 4 |
| Pyridoxal phosphate on K | UNIMOD:46 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| 3'-nitrotyrosine on Y | — | 3 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Carboxylation on K | UNIMOD:299 | 3 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 3 |
| N6-succinyllysine on K | — | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Trimethylation on K | UNIMOD:37 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Glutarylation on K | UNIMOD:1848 | 1 |
| HexNAc on S | UNIMOD:43 | 1 |
| HexNAc on T | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-methacryllysine on K | — | 1 |
| N6-methyllysine on K | UNIMOD:34 | 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
d895ac474a7c704e, written 2026-10-29T10:55:15+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