Generated summary
PXD012753 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 43,949 PSMs, 5,617 peptidoforms and 1,032 protein groups, and the repository holds 2,912 PTM sites for it. 7 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, 7 warnings and 1 for information
high_contamination warning
30.66% of protein intensity in the worst file, 8.28% median across 15 files (DEF-QC-9 v3.5)
30.66% of protein intensity in the worst file, 8.28% median across 15 files (DEF-QC-9 v3.5)
low_core_use warning
13.49 avg cores of 32 allowed (S5)
13.49 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 43949/497729 = 8.83% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 43949/497729 = 8.83% of MS2 identified (S3)
mbr_kept_exceeds_msms warning
kept MBR 41835 > MSMS 25622 (DEF-MBR-KEPT v1)
kept MBR 41835 > MSMS 25622 (DEF-MBR-KEPT v1)
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 5909 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 774 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 5909 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 774 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: 441 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: 441 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
6 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
6 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 | 43,949 |
| Peptidoforms at 1% FDR | 5,617 |
| Protein groups at 1% FDR | 1,032 |
| PTM sites | 2,912 |
| Quantitative values | 103,095 |
| PSMs, all (including decoys and sub-threshold) | 55,461 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 8.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 8.2% |
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
- none
- Instrument vendor
- not recorded
- Runs / samples
- 15 / 15
- 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 | 1,151 |
| Oxidation on M | UNIMOD:35 | 193 |
| Carbamyl on X | UNIMOD:5 | 158 |
| Deamidation on N | UNIMOD:7 | 129 |
| Hydroxylation on P | UNIMOD:35 | 110 |
| Sodium on E | UNIMOD:30 | 89 |
| Deamidation on Q | UNIMOD:7 | 60 |
| Sodium on D | UNIMOD:30 | 56 |
| Ammonia loss on N | UNIMOD:385 | 53 |
| Magnesium on E | UNIMOD:956 | 50 |
| Carbamyl on M | UNIMOD:5 | 47 |
| N-acetylalanine on A | UNIMOD:1 | 42 |
| 4-hydroxyproline on P | UNIMOD:35 | 37 |
| Citrullination on R | UNIMOD:7 | 37 |
| Methylation on K | UNIMOD:34 | 31 |
| Magnesium on D | UNIMOD:956 | 27 |
| N-acetylserine on S | UNIMOD:1 | 24 |
| Acetylation on K | UNIMOD:1 | 17 |
| Hydroxylation on N | UNIMOD:35 | 17 |
| Calcium on E | UNIMOD:951 | 16 |
| Methylation on R | UNIMOD:34 | 15 |
| Calcium on D | UNIMOD:951 | 14 |
| N6-acetyllysine on K | UNIMOD:1 | 10 |
| Trimethylation on K | UNIMOD:37 | 10 |
| Acetylation on X | UNIMOD:1 | 9 |
| Hydroxylation on K | UNIMOD:35 | 9 |
| Carbamyl on R | UNIMOD:5 | 7 |
| Dimethylation on K | UNIMOD:36 | 7 |
| N-acetylmethionine on M | UNIMOD:1 | 7 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 6 |
| Carbamyl on K | UNIMOD:5 | 5 |
| Glutarylation on K | UNIMOD:1848 | 5 |
| N-acetylthreonine on T | UNIMOD:1 | 5 |
| Phosphorylation on S | UNIMOD:21 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N6-methyllysine on K | UNIMOD:34 | 4 |
| Phosphorylation on T | UNIMOD:21 | 4 |
| Phosphoserine on S | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carbamyl on C | UNIMOD:5 | 3 |
| Carboxylation on E | UNIMOD:299 | 3 |
| Hydroxybutyrylation on K | — | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| Phosphothreonine on T | UNIMOD:21 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Ammonia loss on C | UNIMOD:385 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| HexNAc on S | UNIMOD:43 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 2 |
| Water Loss on E | UNIMOD:27 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Carboxylation on D | UNIMOD:299 | 1 |
| Carboxylation on K | UNIMOD:299 | 1 |
| Dimethylation on R | UNIMOD:36 | 1 |
| HexNAc on T | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 1 |
| N6-methacryllysine on K | — | 1 |
| N6-succinyllysine on K | — | 1 |
| Omega-N-methylarginine on R | UNIMOD:34 | 1 |
| Potassium on D | UNIMOD:530 | 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
4abf7e9b06265cc9, written 2026-10-29T09:51:28+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