Generated summary
PXD018399 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and runs that differ in enrichment (other on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 161,098 PSMs, 17,155 peptidoforms and 3,380 protein groups, and the repository holds 5,953 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 161098 where the producer reported 161104 (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 161098 where the producer reported 161104 (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.
low_core_use warning
5.09 avg cores of 32 allowed (S5)
5.09 avg cores of 32 allowed (S5)
mixed_enrichment warning
The runs of this dataset differ in enrichment: 10 run(s) [none]; 10 run(s) [other]. The dataset's own `enrichment` is the producer's declaration and is true of only some runs, so answer any enrichment-dependent question per run from `runs.enrichment`, and never pool its runs as one kind.
The runs of this dataset differ in enrichment: 10 run(s) [none]; 10 run(s) [other]. The dataset's own `enrichment` is the producer's declaration and is true of only some runs, so answer any enrichment-dependent question per run from `runs.enrichment`, and never pool its runs as one kind.
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 12160 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3789 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 12160 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3789 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: 118 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: 118 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
48 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
48 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 | 161,098 |
| Peptidoforms at 1% FDR | 17,155 |
| Protein groups at 1% FDR | 3,380 |
| PTM sites | 5,953 |
| Quantitative values | 274,835 |
| PSMs, all (including decoys and sub-threshold) | 890,994 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 24.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.6% |
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
- other (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0095bcefc3f5
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 2,561 |
| Carbamidomethyl on C | UNIMOD:4 | 1,796 |
| Phosphoserine on S | UNIMOD:21 | 311 |
| Hydroxylation on P | UNIMOD:35 | 273 |
| N-acetylalanine on A | UNIMOD:1 | 156 |
| Acetylation on X | UNIMOD:1 | 117 |
| Phosphorylation on S | UNIMOD:21 | 93 |
| N-acetylmethionine on M | UNIMOD:1 | 72 |
| 4-hydroxyproline on P | UNIMOD:35 | 63 |
| N-acetylserine on S | UNIMOD:1 | 63 |
| Phosphorylation on T | UNIMOD:21 | 63 |
| Phosphothreonine on T | UNIMOD:21 | 42 |
| N6-acetyllysine on K | UNIMOD:1 | 39 |
| Omega-N-methylarginine on R | UNIMOD:34 | 27 |
| Hydroxylation on K | UNIMOD:35 | 24 |
| Acetylation on K | UNIMOD:1 | 23 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 16 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| HexNAc on T | UNIMOD:43 | 13 |
| N6-glutaryllysine on K | — | 13 |
| HexNAc on S | UNIMOD:43 | 12 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 10 |
| Methylation on K | UNIMOD:34 | 10 |
| Phosphorylation on Y | UNIMOD:21 | 9 |
| Malonylation on K | UNIMOD:747 | 7 |
| N-myristoyl glycine on G | UNIMOD:45 | 6 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 6 |
| Dimethylation on K | UNIMOD:36 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-methyllysine on K | UNIMOD:34 | 5 |
| Trimethylation on K | UNIMOD:37 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| (3S)-3-hydroxyasparagine on N | — | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| Dimethylation on R | UNIMOD:36 | 3 |
| Methylation on R | UNIMOD:34 | 3 |
| N6-succinyllysine on K | — | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Deamidated asparagine on N | UNIMOD:7 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-crotonyllysine on K | — | 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
880cd2444991cac9, written 2026-10-29T10:32:05+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