Generated summary
PXD068498 is a DDA label-free dataset (Rattus norvegicus) with 47 runs, 47 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,143,559 PSMs, 24,024 peptidoforms and 3,969 protein groups, and the repository holds 25,440 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 2 for information
count_mismatch warning
The bundle holds 24025 where the producer reported 24024 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 24025 where the producer reported 24024 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
count_mismatch warning
The bundle holds 1.14356e+06 where the producer reported 1.14371e+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 1.14356e+06 where the producer reported 1.14371e+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
14.88 avg cores of 32 allowed (S5)
14.88 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 120471 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 16401 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 120471 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 16401 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: 4712 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: 4712 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD068498:A0A0G2KBA0;A0A8I6G5V5 written 2 times; quant_values: 94 identifier(s), 94 row(s) dropped, e.g. PXD068498:20250109_Sarah_Alberto_KO-108M:label_free:protein_group:PXD068498:A0A0G2KBA0;A0A8I6G5V5: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: 2 identifier(s), 2 row(s) dropped, e.g. PXD068498:A0A0G2KBA0;A0A8I6G5V5 written 2 times; quant_values: 94 identifier(s), 94 row(s) dropped, e.g. PXD068498:20250109_Sarah_Alberto_KO-108M:label_free:protein_group:PXD068498:A0A0G2KBA0;A0A8I6G5V5:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
146 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
146 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 | 1,143,559 |
| Peptidoforms at 1% FDR | 24,024 |
| Protein groups at 1% FDR | 3,969 |
| PTM sites | 25,440 |
| Quantitative values | 1,274,904 |
| PSMs, all (including decoys and sub-threshold) | 2,682,224 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 45.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.1% |
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
- 47 / 47
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0095bcefc3f5
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 8,738 |
| Oxidation on M | UNIMOD:35 | 3,717 |
| Deamidation on Q | UNIMOD:7 | 3,261 |
| Deamidation on N | UNIMOD:7 | 3,222 |
| Citrullination on R | UNIMOD:7 | 1,828 |
| Hydroxylation on P | UNIMOD:35 | 809 |
| Hydroxylation on N | UNIMOD:35 | 522 |
| Ammonia loss on N | UNIMOD:385 | 329 |
| Hydroxylation on K | UNIMOD:35 | 309 |
| Phosphoserine on S | UNIMOD:21 | 229 |
| N-acetylalanine on A | UNIMOD:1 | 153 |
| Acetylation on X | UNIMOD:1 | 142 |
| Fe[II] on D | UNIMOD:952 | 135 |
| Fe[II] on E | UNIMOD:952 | 129 |
| Methylation on K | UNIMOD:34 | 126 |
| Acetylation on K | UNIMOD:1 | 87 |
| Water Loss on E | UNIMOD:27 | 87 |
| Carbamyl on X | UNIMOD:5 | 86 |
| Carbamyl on M | UNIMOD:5 | 79 |
| Phosphorylation on S | UNIMOD:21 | 78 |
| Methylation on R | UNIMOD:34 | 75 |
| Trimethylation on K | UNIMOD:37 | 72 |
| Phosphorylation on T | UNIMOD:21 | 70 |
| Fe[III] on D | UNIMOD:1870 | 69 |
| N6-acetyllysine on K | UNIMOD:1 | 69 |
| N-acetylserine on S | UNIMOD:1 | 67 |
| N-acetylmethionine on M | UNIMOD:1 | 66 |
| Fe[III] on E | UNIMOD:1870 | 64 |
| Phosphothreonine on T | UNIMOD:21 | 50 |
| Ammonia loss on C | UNIMOD:385 | 41 |
| Dimethylation on K | UNIMOD:36 | 41 |
| Dimethylation on R | UNIMOD:36 | 30 |
| Formylation on K | UNIMOD:122 | 29 |
| N6-succinyllysine on K | — | 28 |
| Omega-N-methylarginine on R | UNIMOD:34 | 28 |
| Carbamyl on C | UNIMOD:5 | 24 |
| Deamidated asparagine on N | UNIMOD:7 | 22 |
| N-myristoyl glycine on G | UNIMOD:45 | 20 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| Carboxylation on D | UNIMOD:299 | 18 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 16 |
| Sulfonation on Y | UNIMOD:40 | 16 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 15 |
| Carbamyl on K | UNIMOD:5 | 14 |
| Phosphorylation on Y | UNIMOD:21 | 14 |
| Carbamyl on R | UNIMOD:5 | 13 |
| Carboxylation on E | UNIMOD:299 | 13 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| Nitrosylation on C | UNIMOD:275 | 12 |
| Magnesium on D | UNIMOD:956 | 9 |
| Nitrosylation on Y | UNIMOD:354 | 9 |
| Sodium on E | UNIMOD:30 | 9 |
| Malonylation on K | UNIMOD:747 | 8 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| Carboxylation on K | UNIMOD:299 | 6 |
| Glutarylation on K | UNIMOD:1848 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 5 |
| 3'-nitrotyrosine on Y | — | 4 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Cysteine persulfide on C | UNIMOD:421 | 4 |
| HexNAc on S | UNIMOD:43 | 4 |
| HexNAc on T | UNIMOD:43 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 4 |
| Sodium on D | UNIMOD:30 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Butyrylation on K | UNIMOD:1289 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| Magnesium on E | UNIMOD:956 | 3 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 3 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cysteine methyl ester on C | UNIMOD:34 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Succinylation on K | UNIMOD:64 | 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
d3ce4e0d4a6f0d5a, written 2026-10-29T11:53:12+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group