Generated summary
PXD022737 is a DDA label-free dataset (Rattus norvegicus) with 24 runs, 24 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 627,316 PSMs, 48,822 peptidoforms and 4,672 protein groups, and the repository holds 33,594 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 627316 where the producer reported 627365 (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 627316 where the producer reported 627365 (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
15.27 avg cores of 32 allowed (S5)
15.27 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 132744 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9049 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 132744 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9049 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: 3853 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: 3853 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. PXD022737:A0ACJ1LLN1;Q66H47 written 2 times; quant_values: 24 identifier(s), 24 row(s) dropped, e.g. PXD022737:Lubec_CE123_GE_PFC:label_free:protein_group:PXD022737:A0ACJ1LLN1;Q66H47: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. PXD022737:A0ACJ1LLN1;Q66H47 written 2 times; quant_values: 24 identifier(s), 24 row(s) dropped, e.g. PXD022737:Lubec_CE123_GE_PFC:label_free:protein_group:PXD022737:A0ACJ1LLN1;Q66H47:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
18 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
18 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 | 627,316 |
| Peptidoforms at 1% FDR | 48,822 |
| Protein groups at 1% FDR | 4,672 |
| PTM sites | 33,594 |
| Quantitative values | 958,204 |
| PSMs, all (including decoys and sub-threshold) | 1,333,877 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 90.6% |
| 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
- other
- Instrument vendor
- not recorded
- Runs / samples
- 24 / 24
- Sample metadata
- absent
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 9,586 |
| Oxidation on M | UNIMOD:35 | 7,006 |
| Deamidation on N | UNIMOD:7 | 3,138 |
| Deamidation on Q | UNIMOD:7 | 2,752 |
| Hydroxylation on P | UNIMOD:35 | 1,494 |
| Hydroxylation on N | UNIMOD:35 | 891 |
| Formylation on K | UNIMOD:122 | 862 |
| Ammonia loss on N | UNIMOD:385 | 811 |
| Carbamyl on X | UNIMOD:5 | 778 |
| Citrullination on R | UNIMOD:7 | 603 |
| Ammonia loss on C | UNIMOD:385 | 399 |
| Hydroxylation on K | UNIMOD:35 | 324 |
| Phosphoserine on S | UNIMOD:21 | 272 |
| Fe[III] on D | UNIMOD:1870 | 215 |
| Methylation on K | UNIMOD:34 | 215 |
| Acetylation on X | UNIMOD:1 | 211 |
| Fe[III] on E | UNIMOD:1870 | 202 |
| Phosphorylation on S | UNIMOD:21 | 192 |
| Magnesium on E | UNIMOD:956 | 191 |
| Magnesium on D | UNIMOD:956 | 178 |
| Carboxylation on D | UNIMOD:299 | 168 |
| Sodium on D | UNIMOD:30 | 163 |
| Sodium on E | UNIMOD:30 | 163 |
| Carboxylation on E | UNIMOD:299 | 152 |
| Acetylation on K | UNIMOD:1 | 134 |
| Carbamyl on M | UNIMOD:5 | 131 |
| N-acetylalanine on A | UNIMOD:1 | 127 |
| Methylation on R | UNIMOD:34 | 122 |
| Phosphorylation on T | UNIMOD:21 | 118 |
| Water Loss on E | UNIMOD:27 | 105 |
| Dimethylation on K | UNIMOD:36 | 94 |
| Fe[II] on E | UNIMOD:952 | 75 |
| Fe[II] on D | UNIMOD:952 | 72 |
| Carbamyl on K | UNIMOD:5 | 69 |
| Nitrosylation on Y | UNIMOD:354 | 68 |
| N-acetylmethionine on M | UNIMOD:1 | 66 |
| Phosphothreonine on T | UNIMOD:21 | 66 |
| N-acetylserine on S | UNIMOD:1 | 63 |
| Trimethylation on K | UNIMOD:37 | 57 |
| N6-acetyllysine on K | UNIMOD:1 | 55 |
| Calcium on D | UNIMOD:951 | 48 |
| Calcium on E | UNIMOD:951 | 48 |
| Nitrosylation on C | UNIMOD:275 | 47 |
| Carbamyl on C | UNIMOD:5 | 43 |
| Dimethylation on R | UNIMOD:36 | 41 |
| HexNAc on S | UNIMOD:43 | 35 |
| Succinylation on K | UNIMOD:64 | 32 |
| Carboxylation on K | UNIMOD:299 | 30 |
| Butyrylation on K | UNIMOD:1289 | 29 |
| HexNAc on T | UNIMOD:43 | 26 |
| Phosphorylation on Y | UNIMOD:21 | 26 |
| Cu[I] on D | UNIMOD:531 | 25 |
| Malonylation on K | UNIMOD:747 | 25 |
| Potassium on D | UNIMOD:530 | 25 |
| Sulfonation on Y | UNIMOD:40 | 25 |
| Carbamyl on R | UNIMOD:5 | 23 |
| Cu[I] on E | UNIMOD:531 | 18 |
| N6-succinyllysine on K | — | 17 |
| 4-hydroxyproline on P | UNIMOD:35 | 16 |
| Glutarylation on K | UNIMOD:1848 | 14 |
| Phosphotyrosine on Y | UNIMOD:21 | 14 |
| Potassium on E | UNIMOD:530 | 14 |
| Hydroxybutyrylation on K | — | 13 |
| N-acetylthreonine on T | UNIMOD:1 | 12 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 11 |
| Omega-N-methylarginine on R | UNIMOD:34 | 11 |
| ADP-ribosylation on S | UNIMOD:213 | 9 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 9 |
| Crotonylation on K | UNIMOD:1363 | 9 |
| N-myristoyl glycine on G | UNIMOD:45 | 8 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| Zinc on D | UNIMOD:954 | 5 |
| Zinc on E | UNIMOD:954 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-crotonyllysine on K | — | 2 |
| Allysine on K | UNIMOD:352 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| Pyridoxal phosphate on K | UNIMOD:46 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
eadd237ac086fee7, written 2026-10-29T09:30:14+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