Generated summary
PXD007035 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and runs that differ in enrichment (ubiquitin_GG on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 126,015 PSMs, 23,955 peptidoforms and 3,836 protein groups, and the repository holds 9,575 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
high_contamination warning
5.46% of protein intensity in the worst file, 3.23% median across 12 files (DEF-QC-9 v3.5)
5.46% of protein intensity in the worst file, 3.23% median across 12 files (DEF-QC-9 v3.5)
low_core_use warning
7.23 avg cores of 32 allowed (S5)
7.23 avg cores of 32 allowed (S5)
mixed_enrichment warning
The runs of this dataset differ in enrichment: 6 run(s) [none]; 6 run(s) [ubiquitin_GG]. 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: 6 run(s) [none]; 6 run(s) [ubiquitin_GG]. 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 7082 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3346 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 7082 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3346 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: 114 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: 114 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
36 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
36 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 | 126,015 |
| Peptidoforms at 1% FDR | 23,955 |
| Protein groups at 1% FDR | 3,836 |
| PTM sites | 9,575 |
| Quantitative values | 203,670 |
| PSMs, all (including decoys and sub-threshold) | 1,116,988 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 15.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.2% |
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
- ubiquitin_GG (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 12 / 12
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 852cea5e1cd7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 7,282 |
| Oxidation on M | UNIMOD:35 | 852 |
| N-acetylalanine on A | UNIMOD:1 | 225 |
| Acetylation on X | UNIMOD:1 | 164 |
| Phosphoserine on S | UNIMOD:21 | 139 |
| N-acetylmethionine on M | UNIMOD:1 | 131 |
| Hydroxylation on P | UNIMOD:35 | 91 |
| N-acetylserine on S | UNIMOD:1 | 81 |
| 4-hydroxyproline on P | UNIMOD:35 | 61 |
| N6-acetyllysine on K | UNIMOD:1 | 48 |
| Phosphothreonine on T | UNIMOD:21 | 24 |
| Hydroxylation on K | UNIMOD:35 | 21 |
| Omega-N-methylarginine on R | UNIMOD:34 | 19 |
| N-acetylthreonine on T | UNIMOD:1 | 17 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 16 |
| N-myristoyl glycine on G | UNIMOD:45 | 15 |
| Acetylation on K | UNIMOD:1 | 13 |
| HexNAc on T | UNIMOD:43 | 12 |
| HexNAc on S | UNIMOD:43 | 10 |
| Methylation on K | UNIMOD:34 | 8 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 7 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 7 |
| Dimethylation on R | UNIMOD:36 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-succinyllysine on K | — | 5 |
| Phosphorylation on T | UNIMOD:21 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-lipoyllysine on K | UNIMOD:42 | 4 |
| N6-methyllysine on K | UNIMOD:34 | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| Dimethylation on K | UNIMOD:36 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Phosphorylation on S | UNIMOD:21 | 3 |
| Citrulline on R | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| Methylation on R | UNIMOD:34 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Glutarylation on K | UNIMOD:1848 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| Trimethylation on K | UNIMOD:37 | 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
1db7bc04e237098d, written 2026-10-29T11:45:51+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group