Generated summary
PXD064236 is a DDA label-free dataset (Mus musculus) with 16 runs, 16 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 25,389 PSMs, 1,752 peptidoforms and 509 protein groups, and the repository holds 2,336 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
count_mismatch warning
The bundle holds 25389 where the producer reported 25398 (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 25389 where the producer reported 25398 (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.
cysteine_poor warning
2.43% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
2.43% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
76.43% of protein intensity in the worst file, 58.08% median across 16 files (DEF-QC-9 v3.5)
76.43% of protein intensity in the worst file, 58.08% median across 16 files (DEF-QC-9 v3.5)
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: 25398/1119710 = 2.27% 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: 25398/1119710 = 2.27% of MS2 identified (S3)
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 9857 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 173 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 9857 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 173 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: 381 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: 381 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
27 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
27 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 | 25,389 |
| Peptidoforms at 1% FDR | 1,752 |
| Protein groups at 1% FDR | 509 |
| PTM sites | 2,336 |
| Quantitative values | 35,397 |
| PSMs, all (including decoys and sub-threshold) | 176,958 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 2.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 59.1% |
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
- immunoprecipitation
- Instrument vendor
- not recorded
- Runs / samples
- 16 / 16
- 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 | 271 |
| Deamidation on Q | UNIMOD:7 | 248 |
| Deamidation on N | UNIMOD:7 | 152 |
| Carbamidomethyl on C | UNIMOD:4 | 128 |
| Hydroxylation on P | UNIMOD:35 | 115 |
| Ammonia loss on N | UNIMOD:385 | 62 |
| Citrullination on R | UNIMOD:7 | 57 |
| Fe[III] on D | UNIMOD:1870 | 48 |
| Fe[II] on D | UNIMOD:952 | 43 |
| Water Loss on E | UNIMOD:27 | 42 |
| Fe[III] on E | UNIMOD:1870 | 41 |
| Hydroxylation on N | UNIMOD:35 | 37 |
| Hydroxylation on K | UNIMOD:35 | 36 |
| Fe[II] on E | UNIMOD:952 | 31 |
| Magnesium on D | UNIMOD:956 | 31 |
| Methylation on K | UNIMOD:34 | 29 |
| Dimethylation on R | UNIMOD:36 | 22 |
| N-acetylalanine on A | UNIMOD:1 | 22 |
| Methylation on R | UNIMOD:34 | 18 |
| Carbamyl on X | UNIMOD:5 | 17 |
| Magnesium on E | UNIMOD:956 | 15 |
| N6-acetyllysine on K | UNIMOD:1 | 14 |
| Glu to PyroGlu on Q | UNIMOD:28 | 13 |
| Phosphorylation on T | UNIMOD:21 | 13 |
| Sodium on E | UNIMOD:30 | 13 |
| 4-hydroxyproline on P | UNIMOD:35 | 12 |
| Acetylation on K | UNIMOD:1 | 11 |
| Dimethylation on K | UNIMOD:36 | 11 |
| N-acetylmethionine on M | UNIMOD:1 | 11 |
| N-acetylserine on S | UNIMOD:1 | 11 |
| Phosphorylation on S | UNIMOD:21 | 11 |
| Calcium on E | UNIMOD:951 | 9 |
| Phosphoserine on S | UNIMOD:21 | 9 |
| Carboxylation on D | UNIMOD:299 | 8 |
| Carboxylation on E | UNIMOD:299 | 8 |
| Formylation on K | UNIMOD:122 | 8 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| Sodium on D | UNIMOD:30 | 8 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 7 |
| Calcium on D | UNIMOD:951 | 7 |
| Cu[I] on E | UNIMOD:531 | 7 |
| Trimethylation on K | UNIMOD:37 | 7 |
| HexNAc on T | UNIMOD:43 | 6 |
| Malonylation on K | UNIMOD:747 | 6 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 6 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| Glutarylation on K | UNIMOD:1848 | 5 |
| HexNAc on S | UNIMOD:43 | 5 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 4 |
| Nitrosylation on Y | UNIMOD:354 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| Potassium on D | UNIMOD:530 | 4 |
| Potassium on E | UNIMOD:530 | 4 |
| Butyrylation on K | UNIMOD:1289 | 3 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| Phosphothreonine on T | UNIMOD:21 | 3 |
| Sulfonation on Y | UNIMOD:40 | 3 |
| Acetylation on X | UNIMOD:1 | 2 |
| Carbamyl on K | UNIMOD:5 | 2 |
| Carbamyl on M | UNIMOD:5 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Cu[I] on D | UNIMOD:531 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-acetylthreonine on T | UNIMOD:1 | 2 |
| N6-succinyllysine on K | — | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Omega-N-methylarginine on R | UNIMOD:34 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 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
010bacad9d845fc8, written 2026-10-29T09:39:33+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