Generated summary
PXD027971 is a DDA label-free dataset (Rattus norvegicus) with 15 runs, 15 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 247,005 PSMs, 16,569 peptidoforms and 1,184 protein groups, and the repository holds 16,641 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 1184 where the producer reported 1185 (results.txt: All target protein groups with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 1184 where the producer reported 1185 (results.txt: All target protein groups 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 247005 where the producer reported 249750 (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 247005 where the producer reported 249750 (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.
cysteine_poor warning
3.89% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
3.89% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
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 113894 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 32 duplicate entry for one site and run (identical values; same protein group); 1521 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 113894 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 32 duplicate entry for one site and run (identical values; same protein group); 1521 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: 247 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: 247 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. PXD027971:A0A0G2JZW2;D4A2S8 written 2 times; quant_values: 22 identifier(s), 22 row(s) dropped, e.g. PXD027971:QEp20-4004_Leslie_Young1_DTT_TiO2:label_free:protein_group:PXD027971:A0A0G2JZW2;D4A2S8: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. PXD027971:A0A0G2JZW2;D4A2S8 written 2 times; quant_values: 22 identifier(s), 22 row(s) dropped, e.g. PXD027971:QEp20-4004_Leslie_Young1_DTT_TiO2:label_free:protein_group:PXD027971:A0A0G2JZW2;D4A2S8:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
175 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
175 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 | 247,005 |
| Peptidoforms at 1% FDR | 16,569 |
| Protein groups at 1% FDR | 1,184 |
| PTM sites | 16,641 |
| Quantitative values | 118,799 |
| PSMs, all (including decoys and sub-threshold) | 528,295 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 25.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.2% |
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
- phospho
- Instrument vendor
- not recorded
- Runs / samples
- 15 / 15
- Sample metadata
- absent
- 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 | 3,655 |
| Phosphoserine on S | UNIMOD:21 | 1,616 |
| Deamidation on Q | UNIMOD:7 | 1,257 |
| Phosphorylation on T | UNIMOD:21 | 1,240 |
| Fe[II] on E | UNIMOD:952 | 786 |
| Oxidation on M | UNIMOD:35 | 769 |
| Deamidation on N | UNIMOD:7 | 706 |
| Carbamidomethyl on C | UNIMOD:4 | 571 |
| Fe[II] on D | UNIMOD:952 | 537 |
| Hydroxylation on P | UNIMOD:35 | 427 |
| Fe[III] on E | UNIMOD:1870 | 426 |
| Citrullination on R | UNIMOD:7 | 362 |
| Magnesium on E | UNIMOD:956 | 306 |
| Sodium on E | UNIMOD:30 | 286 |
| Fe[III] on D | UNIMOD:1870 | 272 |
| Phosphothreonine on T | UNIMOD:21 | 240 |
| Sulfonation on Y | UNIMOD:40 | 237 |
| Calcium on E | UNIMOD:951 | 217 |
| Phosphorylation on Y | UNIMOD:21 | 211 |
| Magnesium on D | UNIMOD:956 | 200 |
| Sodium on D | UNIMOD:30 | 195 |
| Calcium on D | UNIMOD:951 | 146 |
| Hydroxylation on K | UNIMOD:35 | 146 |
| Cu[I] on E | UNIMOD:531 | 134 |
| Potassium on E | UNIMOD:530 | 127 |
| Ammonia loss on N | UNIMOD:385 | 122 |
| Hydroxylation on N | UNIMOD:35 | 114 |
| Cu[I] on D | UNIMOD:531 | 94 |
| Water Loss on E | UNIMOD:27 | 83 |
| Potassium on D | UNIMOD:530 | 81 |
| Methylation on K | UNIMOD:34 | 58 |
| Carbamyl on X | UNIMOD:5 | 54 |
| Carboxylation on E | UNIMOD:299 | 49 |
| Succinylation on K | UNIMOD:64 | 49 |
| HexNAc on S | UNIMOD:43 | 44 |
| Zinc on E | UNIMOD:954 | 39 |
| Crotonylation on K | UNIMOD:1363 | 38 |
| Dimethylation on K | UNIMOD:36 | 37 |
| N-acetylalanine on A | UNIMOD:1 | 37 |
| Zinc on D | UNIMOD:954 | 37 |
| 4-hydroxyproline on P | UNIMOD:35 | 35 |
| Carboxylation on D | UNIMOD:299 | 35 |
| Acetylation on K | UNIMOD:1 | 34 |
| Acetylation on X | UNIMOD:1 | 31 |
| Malonylation on K | UNIMOD:747 | 29 |
| HexNAc on T | UNIMOD:43 | 26 |
| Carbamyl on K | UNIMOD:5 | 25 |
| Glutarylation on K | UNIMOD:1848 | 25 |
| N-acetylserine on S | UNIMOD:1 | 25 |
| Formylation on K | UNIMOD:122 | 24 |
| Methylation on R | UNIMOD:34 | 22 |
| Phosphotyrosine on Y | UNIMOD:21 | 21 |
| N6-acetyllysine on K | UNIMOD:1 | 20 |
| Trimethylation on K | UNIMOD:37 | 20 |
| Hydroxybutyrylation on K | — | 17 |
| Nitrosylation on Y | UNIMOD:354 | 17 |
| Pyridoxal phosphate on K | UNIMOD:46 | 16 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 14 |
| N-acetylmethionine on M | UNIMOD:1 | 14 |
| Dimethylation on R | UNIMOD:36 | 10 |
| Carboxylation on K | UNIMOD:299 | 9 |
| Omega-N-methylarginine on R | UNIMOD:34 | 9 |
| Carbamyl on R | UNIMOD:5 | 8 |
| Ammonia loss on C | UNIMOD:385 | 6 |
| Carbamyl on M | UNIMOD:5 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 4 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| N-acetylthreonine on T | UNIMOD:1 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| N6-succinyllysine on K | — | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Sulfotyrosine on Y | UNIMOD:40 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglycine on G | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-methylhistidine on H | 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
551535c718e006bd, written 2026-10-29T11:00:41+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, protein_groups_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group