Generated summary
PXD032044 is a DDA label-free dataset (Rattus norvegicus) with 44 runs, 44 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 871,294 PSMs, 38,822 peptidoforms and 3,003 protein groups, and the repository holds 31,761 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 871294 where the producer reported 871682 (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 871294 where the producer reported 871682 (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.
high_contamination warning
5.53% of protein intensity in the worst file, 1.58% median across 44 files (DEF-QC-9 v3.5)
5.53% of protein intensity in the worst file, 1.58% median across 44 files (DEF-QC-9 v3.5)
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 134777 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 3483 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 134777 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 3483 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: 8728 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: 8728 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: 3 identifier(s), 3 row(s) dropped, e.g. PXD032044:A0A8I6AJU0;D4ADG5 written 2 times; quant_values: 132 identifier(s), 132 row(s) dropped, e.g. PXD032044:8540_22-S-P_:label_free:protein_group:PXD032044:A0A8I6AJU0;D4ADG5: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: 3 identifier(s), 3 row(s) dropped, e.g. PXD032044:A0A8I6AJU0;D4ADG5 written 2 times; quant_values: 132 identifier(s), 132 row(s) dropped, e.g. PXD032044:8540_22-S-P_:label_free:protein_group:PXD032044:A0A8I6AJU0;D4ADG5:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
76 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
76 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 | 871,294 |
| Peptidoforms at 1% FDR | 38,822 |
| Protein groups at 1% FDR | 3,003 |
| PTM sites | 31,761 |
| Quantitative values | 866,759 |
| PSMs, all (including decoys and sub-threshold) | 2,140,456 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 63.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.2% |
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
- 44 / 44
- 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 | 8,352 |
| Oxidation on M | UNIMOD:35 | 5,744 |
| Deamidation on N | UNIMOD:7 | 2,026 |
| Deamidation on Q | UNIMOD:7 | 1,691 |
| Carbamyl on K | UNIMOD:5 | 1,601 |
| Carbamyl on X | UNIMOD:5 | 1,296 |
| Hydroxylation on P | UNIMOD:35 | 875 |
| Hydroxylation on N | UNIMOD:35 | 760 |
| Carbamyl on M | UNIMOD:5 | 718 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 601 |
| Methylation on K | UNIMOD:34 | 553 |
| Ammonia loss on N | UNIMOD:385 | 543 |
| Formylation on K | UNIMOD:122 | 536 |
| Citrullination on R | UNIMOD:7 | 462 |
| Hydroxylation on K | UNIMOD:35 | 446 |
| Acetylation on K | UNIMOD:1 | 310 |
| Glutarylation on K | UNIMOD:1848 | 235 |
| Methylation on R | UNIMOD:34 | 232 |
| Sodium on E | UNIMOD:30 | 208 |
| Water Loss on E | UNIMOD:27 | 197 |
| Trimethylation on K | UNIMOD:37 | 196 |
| Carbamyl on R | UNIMOD:5 | 184 |
| Phosphorylation on S | UNIMOD:21 | 183 |
| Phosphoserine on S | UNIMOD:21 | 175 |
| Dimethylation on K | UNIMOD:36 | 171 |
| Magnesium on E | UNIMOD:956 | 149 |
| Carboxylation on E | UNIMOD:299 | 134 |
| Sodium on D | UNIMOD:30 | 132 |
| Ammonia loss on C | UNIMOD:385 | 125 |
| Succinylation on K | UNIMOD:64 | 110 |
| Phosphorylation on T | UNIMOD:21 | 109 |
| Carboxylation on D | UNIMOD:299 | 108 |
| Calcium on E | UNIMOD:951 | 92 |
| Magnesium on D | UNIMOD:956 | 88 |
| N6-acetyllysine on K | UNIMOD:1 | 88 |
| Carbamyl on C | UNIMOD:5 | 86 |
| Malonylation on K | UNIMOD:747 | 79 |
| Dimethylation on R | UNIMOD:36 | 76 |
| Potassium on E | UNIMOD:530 | 76 |
| Nitrosylation on Y | UNIMOD:354 | 74 |
| Butyrylation on K | UNIMOD:1289 | 67 |
| Calcium on D | UNIMOD:951 | 65 |
| Acetylation on X | UNIMOD:1 | 64 |
| Crotonylation on K | UNIMOD:1363 | 64 |
| Carboxylation on K | UNIMOD:299 | 62 |
| Cu[I] on E | UNIMOD:531 | 62 |
| Fe[III] on E | UNIMOD:1870 | 61 |
| Cu[I] on D | UNIMOD:531 | 56 |
| N-acetylalanine on A | UNIMOD:1 | 53 |
| Fe[II] on E | UNIMOD:952 | 48 |
| Fe[III] on D | UNIMOD:1870 | 47 |
| Phosphothreonine on T | UNIMOD:21 | 45 |
| Potassium on D | UNIMOD:530 | 44 |
| 4-hydroxyproline on P | UNIMOD:35 | 37 |
| Sulfonation on Y | UNIMOD:40 | 37 |
| HexNAc on S | UNIMOD:43 | 36 |
| Hydroxybutyrylation on K | — | 36 |
| N-acetylserine on S | UNIMOD:1 | 32 |
| Nitrosylation on C | UNIMOD:275 | 32 |
| Fe[II] on D | UNIMOD:952 | 31 |
| Phosphorylation on Y | UNIMOD:21 | 31 |
| Zinc on D | UNIMOD:954 | 26 |
| Zinc on E | UNIMOD:954 | 25 |
| N-acetylmethionine on M | UNIMOD:1 | 16 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 16 |
| N6-succinyllysine on K | — | 16 |
| HexNAc on T | UNIMOD:43 | 15 |
| Phosphotyrosine on Y | UNIMOD:21 | 13 |
| ADP-ribosylation on S | UNIMOD:213 | 12 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 12 |
| Omega-N-methylarginine on R | UNIMOD:34 | 10 |
| Deamidated asparagine on N | UNIMOD:7 | 9 |
| Pyridoxal phosphate on K | UNIMOD:46 | 9 |
| Glu to PyroGlu on Q | UNIMOD:28 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| N6-malonyllysine on K | — | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| N-acetylthreonine on T | UNIMOD:1 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Cysteine persulfide on C | UNIMOD:421 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| N6-glutaryllysine on K | — | 2 |
| N6-methacryllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
db49fdc46ebec6b7, written 2026-10-29T12:33:48+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