Generated summary
PXD028157 is a DDA label-free dataset (Rattus norvegicus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,351,827 PSMs, 56,370 peptidoforms and 5,126 protein groups, and the repository holds 43,069 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 1.35183e+06 where the producer reported 1.35192e+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 1.35183e+06 where the producer reported 1.35192e+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.
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 348212 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 duplicate entry for one site and run (identical values; same protein group); 11567 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 348212 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 duplicate entry for one site and run (identical values; same protein group); 11567 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: 10979 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: 10979 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. PXD028157:A0A0G2JTA4;A0ABK0LK09 written 2 times; quant_values: 60 identifier(s), 60 row(s) dropped, e.g. PXD028157:DAT_KO_R1_CM_LA_1:label_free:protein_group:PXD028157:A0A0G2JTA4;A0ABK0LK09: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. PXD028157:A0A0G2JTA4;A0ABK0LK09 written 2 times; quant_values: 60 identifier(s), 60 row(s) dropped, e.g. PXD028157:DAT_KO_R1_CM_LA_1:label_free:protein_group:PXD028157:A0A0G2JTA4;A0ABK0LK09:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
282 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
282 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 | 1,351,827 |
| Peptidoforms at 1% FDR | 56,370 |
| Protein groups at 1% FDR | 5,126 |
| PTM sites | 43,069 |
| Quantitative values | 1,006,784 |
| PSMs, all (including decoys and sub-threshold) | 2,155,388 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 67.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
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
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 852cea5e1cd7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,452 |
| Deamidation on Q | UNIMOD:7 | 9,361 |
| Deamidation on N | UNIMOD:7 | 6,631 |
| Oxidation on M | UNIMOD:35 | 3,278 |
| Citrullination on R | UNIMOD:7 | 2,009 |
| Ammonia loss on N | UNIMOD:385 | 900 |
| Hydroxylation on P | UNIMOD:35 | 709 |
| Fe[III] on E | UNIMOD:1870 | 667 |
| Fe[III] on D | UNIMOD:1870 | 600 |
| Formylation on K | UNIMOD:122 | 557 |
| Hydroxylation on N | UNIMOD:35 | 391 |
| Ammonia loss on C | UNIMOD:385 | 385 |
| Fe[II] on E | UNIMOD:952 | 371 |
| Fe[II] on D | UNIMOD:952 | 359 |
| Phosphoserine on S | UNIMOD:21 | 346 |
| Sodium on D | UNIMOD:30 | 301 |
| Acetylation on X | UNIMOD:1 | 282 |
| Methylation on K | UNIMOD:34 | 250 |
| Sodium on E | UNIMOD:30 | 250 |
| Water Loss on E | UNIMOD:27 | 214 |
| Methylation on R | UNIMOD:34 | 212 |
| Phosphorylation on S | UNIMOD:21 | 195 |
| Dimethylation on K | UNIMOD:36 | 191 |
| Dimethylation on R | UNIMOD:36 | 178 |
| N-acetylalanine on A | UNIMOD:1 | 168 |
| Carbamyl on X | UNIMOD:5 | 158 |
| Hydroxylation on K | UNIMOD:35 | 156 |
| Magnesium on D | UNIMOD:956 | 147 |
| Magnesium on E | UNIMOD:956 | 139 |
| Phosphorylation on T | UNIMOD:21 | 139 |
| Acetylation on K | UNIMOD:1 | 110 |
| Calcium on D | UNIMOD:951 | 108 |
| Carbamyl on M | UNIMOD:5 | 105 |
| N-acetylmethionine on M | UNIMOD:1 | 97 |
| Calcium on E | UNIMOD:951 | 93 |
| N6-acetyllysine on K | UNIMOD:1 | 86 |
| N-acetylserine on S | UNIMOD:1 | 73 |
| Phosphothreonine on T | UNIMOD:21 | 73 |
| Carboxylation on D | UNIMOD:299 | 56 |
| Nitrosylation on C | UNIMOD:275 | 46 |
| Carboxylation on E | UNIMOD:299 | 44 |
| Potassium on D | UNIMOD:530 | 42 |
| Carbamyl on C | UNIMOD:5 | 40 |
| Carbamyl on K | UNIMOD:5 | 40 |
| Potassium on E | UNIMOD:530 | 39 |
| Trimethylation on K | UNIMOD:37 | 39 |
| Zinc on D | UNIMOD:954 | 37 |
| Cu[I] on E | UNIMOD:531 | 34 |
| Zinc on E | UNIMOD:954 | 33 |
| N6-succinyllysine on K | — | 32 |
| Cu[I] on D | UNIMOD:531 | 29 |
| Deamidated asparagine on N | UNIMOD:7 | 29 |
| Omega-N-methylarginine on R | UNIMOD:34 | 29 |
| Phosphorylation on Y | UNIMOD:21 | 27 |
| HexNAc on S | UNIMOD:43 | 26 |
| 4-hydroxyproline on P | UNIMOD:35 | 23 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 23 |
| Sulfonation on Y | UNIMOD:40 | 22 |
| Glutarylation on K | UNIMOD:1848 | 19 |
| Carboxylation on K | UNIMOD:299 | 18 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 17 |
| Nitrosylation on Y | UNIMOD:354 | 17 |
| HexNAc on T | UNIMOD:43 | 16 |
| Hydroxybutyrylation on K | — | 15 |
| Butyrylation on K | UNIMOD:1289 | 14 |
| Malonylation on K | UNIMOD:747 | 14 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| Phosphotyrosine on Y | UNIMOD:21 | 12 |
| Carbamyl on R | UNIMOD:5 | 11 |
| Succinylation on K | UNIMOD:64 | 11 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 10 |
| Crotonylation on K | UNIMOD:1363 | 10 |
| N-acetylvaline on V | UNIMOD:1 | 9 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| Citrulline on R | UNIMOD:7 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-glutaryllysine on K | — | 5 |
| Pyridoxal phosphate on K | UNIMOD:46 | 5 |
| 3'-nitrotyrosine on Y | — | 4 |
| Cysteine persulfide on C | UNIMOD:421 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 4 |
| N6-methyllysine on K | UNIMOD:34 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Allysine on K | UNIMOD:352 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| N6-methacryllysine on K | — | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| O-palmitoyl serine on S | UNIMOD:47 | 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
76713d68856fcd47, written 2026-10-29T12:25:56+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