Generated summary
PXD017058 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 182,903 PSMs, 28,688 peptidoforms and 2,419 protein groups, and the repository holds 19,068 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 1 for information
count_mismatch warning
The bundle holds 182903 where the producer reported 182907 (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 182903 where the producer reported 182907 (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
44.78% of protein intensity in the worst file, 29.30% median across 9 files (DEF-QC-9 v3.5)
44.78% of protein intensity in the worst file, 29.30% median across 9 files (DEF-QC-9 v3.5)
low_core_use warning
15.53 avg cores of 32 allowed (S5)
15.53 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 37261 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1685 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 37261 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1685 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: 723 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: 723 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.
occupancy_decoy_groups info
32 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
32 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 | 182,903 |
| Peptidoforms at 1% FDR | 28,688 |
| Protein groups at 1% FDR | 2,419 |
| PTM sites | 19,068 |
| Quantitative values | 234,952 |
| PSMs, all (including decoys and sub-threshold) | 289,896 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 43.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 21.5% |
How it was measured
- Organism searched
- Mus musculus (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
- 9 / 9
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 6,911 |
| Oxidation on M | UNIMOD:35 | 2,083 |
| Deamidation on N | UNIMOD:7 | 1,545 |
| Hydroxylation on P | UNIMOD:35 | 613 |
| Carbamyl on X | UNIMOD:5 | 353 |
| Deamidation on Q | UNIMOD:7 | 339 |
| Ammonia loss on C | UNIMOD:385 | 313 |
| Ammonia loss on N | UNIMOD:385 | 198 |
| Sodium on E | UNIMOD:30 | 187 |
| Fe[III] on E | UNIMOD:1870 | 160 |
| Fe[III] on D | UNIMOD:1870 | 155 |
| Sodium on D | UNIMOD:30 | 154 |
| Hydroxylation on K | UNIMOD:35 | 152 |
| Hydroxylation on N | UNIMOD:35 | 151 |
| Fe[II] on E | UNIMOD:952 | 143 |
| Fe[II] on D | UNIMOD:952 | 139 |
| N-acetylalanine on A | UNIMOD:1 | 121 |
| 4-hydroxyproline on P | UNIMOD:35 | 113 |
| Citrullination on R | UNIMOD:7 | 108 |
| Calcium on D | UNIMOD:951 | 106 |
| Calcium on E | UNIMOD:951 | 84 |
| Phosphoserine on S | UNIMOD:21 | 74 |
| Carbamyl on K | UNIMOD:5 | 59 |
| Methylation on K | UNIMOD:34 | 49 |
| N-acetylserine on S | UNIMOD:1 | 45 |
| Acetylation on X | UNIMOD:1 | 38 |
| Phosphorylation on S | UNIMOD:21 | 37 |
| Carbamyl on M | UNIMOD:5 | 36 |
| N-acetylmethionine on M | UNIMOD:1 | 34 |
| Water Loss on E | UNIMOD:27 | 29 |
| Magnesium on E | UNIMOD:956 | 27 |
| Phosphorylation on T | UNIMOD:21 | 22 |
| Methylation on R | UNIMOD:34 | 18 |
| Crotonylation on K | UNIMOD:1363 | 16 |
| HexNAc on T | UNIMOD:43 | 15 |
| Acetylation on K | UNIMOD:1 | 14 |
| Carbamyl on R | UNIMOD:5 | 14 |
| N6-acetyllysine on K | UNIMOD:1 | 14 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 13 |
| HexNAc on S | UNIMOD:43 | 13 |
| Magnesium on D | UNIMOD:956 | 13 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| Sulfonation on Y | UNIMOD:40 | 13 |
| Phosphothreonine on T | UNIMOD:21 | 12 |
| Potassium on D | UNIMOD:530 | 12 |
| Dimethylation on K | UNIMOD:36 | 10 |
| Dimethylation on R | UNIMOD:36 | 8 |
| Formylation on K | UNIMOD:122 | 8 |
| 3-hydroxyproline on P | UNIMOD:35 | 7 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 7 |
| Potassium on E | UNIMOD:530 | 7 |
| 5-hydroxylysine on K | UNIMOD:35 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 6 |
| Phosphorylation on Y | UNIMOD:21 | 6 |
| Carbamyl on C | UNIMOD:5 | 5 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 5 |
| Glutarylation on K | UNIMOD:1848 | 5 |
| Malonylation on K | UNIMOD:747 | 5 |
| Carboxylation on E | UNIMOD:299 | 4 |
| Carboxylation on K | UNIMOD:299 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-methyllysine on K | UNIMOD:34 | 4 |
| N6-succinyllysine on K | — | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Trimethylation on K | UNIMOD:37 | 4 |
| 4-carboxyglutamate on E | UNIMOD:299 | 3 |
| Carboxylation on D | UNIMOD:299 | 3 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| Phosphotyrosine on Y | UNIMOD:21 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3R)-3-hydroxyasparagine on N | UNIMOD:35 | 1 |
| (3R)-3-hydroxyaspartate on D | UNIMOD:35 | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-methacryllysine on K | — | 1 |
| Nitrosylation on Y | UNIMOD:354 | 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
cf165a78fa2d35d2, written 2026-10-29T09:25:01+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