Generated summary
PXD044453 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 164,088 PSMs, 2,156 peptidoforms and 350 protein groups, and the repository holds 4,896 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 2156 where the producer reported 2155 (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 2156 where the producer reported 2155 (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 164088 where the producer reported 164089 (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 164088 where the producer reported 164089 (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
8.62% of protein intensity in the worst file, 1.34% median across 40 files (DEF-QC-9 v3.5)
8.62% of protein intensity in the worst file, 1.34% median across 40 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 18496 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 112 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 18496 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 112 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: 484 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: 484 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
112 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
112 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 | 164,088 |
| Peptidoforms at 1% FDR | 2,156 |
| Protein groups at 1% FDR | 350 |
| PTM sites | 4,896 |
| Quantitative values | 167,758 |
| PSMs, all (including decoys and sub-threshold) | 576,116 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 23.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.7% |
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
- 40 / 40
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- a086cd029e63
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 1,507 |
| Oxidation on M | UNIMOD:35 | 692 |
| Deamidation on N | UNIMOD:7 | 340 |
| Deamidation on Q | UNIMOD:7 | 269 |
| Fe[III] on E | UNIMOD:1870 | 236 |
| Carbamyl on X | UNIMOD:5 | 216 |
| Hydroxylation on P | UNIMOD:35 | 210 |
| Fe[III] on D | UNIMOD:1870 | 178 |
| Hydroxylation on N | UNIMOD:35 | 130 |
| Citrullination on R | UNIMOD:7 | 100 |
| Ammonia loss on N | UNIMOD:385 | 86 |
| Fe[II] on E | UNIMOD:952 | 77 |
| Hydroxylation on K | UNIMOD:35 | 70 |
| Phosphoserine on S | UNIMOD:21 | 66 |
| Fe[II] on D | UNIMOD:952 | 61 |
| Carbamyl on K | UNIMOD:5 | 43 |
| Carbamyl on C | UNIMOD:5 | 34 |
| Formylation on K | UNIMOD:122 | 28 |
| Methylation on K | UNIMOD:34 | 28 |
| Carbamyl on R | UNIMOD:5 | 27 |
| Magnesium on E | UNIMOD:956 | 26 |
| Sodium on E | UNIMOD:30 | 25 |
| Phosphorylation on S | UNIMOD:21 | 23 |
| Calcium on E | UNIMOD:951 | 21 |
| Acetylation on K | UNIMOD:1 | 18 |
| Ammonia loss on C | UNIMOD:385 | 17 |
| Carbamyl on M | UNIMOD:5 | 17 |
| Magnesium on D | UNIMOD:956 | 17 |
| Calcium on D | UNIMOD:951 | 15 |
| Dimethylation on R | UNIMOD:36 | 14 |
| Nitrosylation on C | UNIMOD:275 | 13 |
| Sodium on D | UNIMOD:30 | 13 |
| Water Loss on E | UNIMOD:27 | 13 |
| Dimethylation on K | UNIMOD:36 | 12 |
| Methylation on R | UNIMOD:34 | 12 |
| Phosphorylation on T | UNIMOD:21 | 12 |
| 4-hydroxyproline on P | UNIMOD:35 | 11 |
| Butyrylation on K | UNIMOD:1289 | 10 |
| N6-acetyllysine on K | UNIMOD:1 | 10 |
| Trimethylation on K | UNIMOD:37 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 9 |
| Potassium on E | UNIMOD:530 | 9 |
| HexNAc on T | UNIMOD:43 | 8 |
| HexNAc on S | UNIMOD:43 | 7 |
| N-acetylalanine on A | UNIMOD:1 | 7 |
| N-acetylserine on S | UNIMOD:1 | 7 |
| Potassium on D | UNIMOD:530 | 7 |
| Glu to PyroGlu on Q | UNIMOD:28 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Hydroxybutyrylation on K | — | 5 |
| Acetylation on X | UNIMOD:1 | 4 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| N6-succinyllysine on K | — | 4 |
| Omega-N-methylarginine on R | UNIMOD:34 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 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
afd56c163a4092b0, written 2026-10-29T11:18:05+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