Generated summary
PXD043779 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 272,721 PSMs, 20,697 peptidoforms and 2,378 protein groups, and the repository holds 11,337 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 272721 where the producer reported 272749 (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 272721 where the producer reported 272749 (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
11.69% of protein intensity in the worst file, 5.47% median across 24 files (DEF-QC-9 v3.5)
11.69% of protein intensity in the worst file, 5.47% median across 24 files (DEF-QC-9 v3.5)
low_core_use warning
5.82 avg cores of 32 allowed (S5)
5.82 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 34450 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5290 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 34450 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5290 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: 838 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: 838 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
78 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
78 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 | 272,721 |
| Peptidoforms at 1% FDR | 20,697 |
| Protein groups at 1% FDR | 2,378 |
| PTM sites | 11,337 |
| Quantitative values | 549,198 |
| PSMs, all (including decoys and sub-threshold) | 388,261 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 53.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 4.8% |
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
- 24 / 24
- 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 |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 3,787 |
| Carbamidomethyl on C | UNIMOD:4 | 3,785 |
| Deamidation on N | UNIMOD:7 | 619 |
| Hydroxylation on P | UNIMOD:35 | 460 |
| Methylation on K | UNIMOD:34 | 228 |
| Deamidation on Q | UNIMOD:7 | 219 |
| Hydroxylation on N | UNIMOD:35 | 199 |
| N-acetylalanine on A | UNIMOD:1 | 151 |
| Carbamyl on X | UNIMOD:5 | 131 |
| Ammonia loss on N | UNIMOD:385 | 127 |
| Ammonia loss on C | UNIMOD:385 | 118 |
| Hydroxylation on K | UNIMOD:35 | 111 |
| Methylation on R | UNIMOD:34 | 111 |
| Carbamyl on M | UNIMOD:5 | 94 |
| Citrullination on R | UNIMOD:7 | 66 |
| N-acetylserine on S | UNIMOD:1 | 59 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 52 |
| N-acetylmethionine on M | UNIMOD:1 | 46 |
| Acetylation on X | UNIMOD:1 | 44 |
| Phosphoserine on S | UNIMOD:21 | 38 |
| Carbamyl on K | UNIMOD:5 | 29 |
| Acetylation on K | UNIMOD:1 | 28 |
| N6-acetyllysine on K | UNIMOD:1 | 26 |
| N5-methylglutamine on Q | UNIMOD:34 | 18 |
| Sodium on D | UNIMOD:30 | 18 |
| Dimethylation on K | UNIMOD:36 | 17 |
| N-acetylthreonine on T | UNIMOD:1 | 17 |
| N6-methyllysine on K | UNIMOD:34 | 16 |
| Dimethylation on R | UNIMOD:36 | 15 |
| Magnesium on D | UNIMOD:956 | 15 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 13 |
| Carbamyl on C | UNIMOD:5 | 12 |
| Glutarylation on K | UNIMOD:1848 | 12 |
| Magnesium on E | UNIMOD:956 | 12 |
| Phosphorylation on S | UNIMOD:21 | 12 |
| Sodium on E | UNIMOD:30 | 12 |
| Nitrosylation on Y | UNIMOD:354 | 10 |
| Water Loss on E | UNIMOD:27 | 10 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 9 |
| Sulfonation on Y | UNIMOD:40 | 9 |
| Phosphothreonine on T | UNIMOD:21 | 8 |
| Trimethylation on K | UNIMOD:37 | 8 |
| Hydroxybutyrylation on K | — | 7 |
| Phosphorylation on T | UNIMOD:21 | 7 |
| Butyrylation on K | UNIMOD:1289 | 6 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 6 |
| Nitrosylation on C | UNIMOD:275 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| HexNAc on T | UNIMOD:43 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| HexNAc on S | UNIMOD:43 | 2 |
| Malonylation on K | UNIMOD:747 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-methacryllysine on K | — | 2 |
| N6-succinyllysine on K | — | 2 |
| Phosphotyrosine on Y | UNIMOD:21 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| Phosphorylation on Y | UNIMOD:21 | 1 |
| Succinylation on K | UNIMOD:64 | 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
6597db5f357e68d2, written 2026-10-29T09:18:56+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