Generated summary
PXD058855 is a DDA label-free dataset (Homo sapiens) with 25 runs, 25 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 78,573 PSMs, 5,632 peptidoforms and 1,083 protein groups, and the repository holds 4,120 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 5632 where the producer reported 5631 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 5632 where the producer reported 5631 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
high_contamination warning
8.30% of protein intensity in the worst file, 5.36% median across 25 files (DEF-QC-9 v3.5)
8.30% of protein intensity in the worst file, 5.36% median across 25 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: 78573/1675751 = 4.69% 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: 78573/1675751 = 4.69% 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 19319 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1140 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 19319 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1140 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: 998 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: 998 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 | 78,573 |
| Peptidoforms at 1% FDR | 5,632 |
| Protein groups at 1% FDR | 1,083 |
| PTM sites | 4,120 |
| Quantitative values | 96,797 |
| PSMs, all (including decoys and sub-threshold) | 596,339 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 4.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.4% |
How it was measured
- Organism searched
- Homo sapiens (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 25 / 25
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- a086cd029e63
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 1,222 |
| Oxidation on M | UNIMOD:35 | 353 |
| Deamidation on Q | UNIMOD:7 | 274 |
| Deamidation on N | UNIMOD:7 | 264 |
| N-acetylalanine on A | UNIMOD:1 | 92 |
| Ammonia loss on N | UNIMOD:385 | 74 |
| Hydroxylation on N | UNIMOD:35 | 67 |
| Magnesium on E | UNIMOD:956 | 61 |
| Citrullination on R | UNIMOD:7 | 56 |
| Sodium on E | UNIMOD:30 | 56 |
| Formylation on K | UNIMOD:122 | 47 |
| Magnesium on D | UNIMOD:956 | 47 |
| Phosphoserine on S | UNIMOD:21 | 42 |
| Fe[II] on E | UNIMOD:952 | 39 |
| Hydroxylation on P | UNIMOD:35 | 39 |
| Calcium on E | UNIMOD:951 | 36 |
| Fe[III] on E | UNIMOD:1870 | 36 |
| Ammonia loss on C | UNIMOD:385 | 32 |
| Sodium on D | UNIMOD:30 | 30 |
| Methylation on K | UNIMOD:34 | 29 |
| N-acetylserine on S | UNIMOD:1 | 29 |
| Calcium on D | UNIMOD:951 | 28 |
| Fe[II] on D | UNIMOD:952 | 27 |
| Methylation on R | UNIMOD:34 | 27 |
| Hydroxylation on K | UNIMOD:35 | 26 |
| Carboxylation on E | UNIMOD:299 | 25 |
| Carbamyl on X | UNIMOD:5 | 23 |
| Fe[III] on D | UNIMOD:1870 | 23 |
| Acetylation on K | UNIMOD:1 | 22 |
| Carbamyl on M | UNIMOD:5 | 17 |
| Carbamyl on K | UNIMOD:5 | 14 |
| N6-acetyllysine on K | UNIMOD:1 | 14 |
| Potassium on E | UNIMOD:530 | 14 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 12 |
| Potassium on D | UNIMOD:530 | 12 |
| Carboxylation on D | UNIMOD:299 | 10 |
| Phosphorylation on S | UNIMOD:21 | 10 |
| Dimethylation on R | UNIMOD:36 | 9 |
| N-acetylmethionine on M | UNIMOD:1 | 9 |
| Omega-N-methylarginine on R | UNIMOD:34 | 9 |
| Water Loss on E | UNIMOD:27 | 9 |
| Dimethylation on K | UNIMOD:36 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 8 |
| N-acetylthreonine on T | UNIMOD:1 | 7 |
| Phosphorylation on T | UNIMOD:21 | 7 |
| Acetylation on X | UNIMOD:1 | 6 |
| Carbamyl on R | UNIMOD:5 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 5 |
| N6-glutaryllysine on K | — | 5 |
| Phosphothreonine on T | UNIMOD:21 | 5 |
| Trimethylation on K | UNIMOD:37 | 5 |
| 4-hydroxyproline on P | UNIMOD:35 | 3 |
| Butyrylation on K | UNIMOD:1289 | 3 |
| Carbamyl on C | UNIMOD:5 | 3 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Cu[I] on E | UNIMOD:531 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| HexNAc on S | UNIMOD:43 | 3 |
| N6-methyllysine on K | UNIMOD:34 | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| Pyridoxal phosphate on K | UNIMOD:46 | 2 |
| Cu[I] on D | UNIMOD:531 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on T | UNIMOD:43 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| N6-succinyllysine on K | — | 1 |
| Phosphorylation on Y | UNIMOD:21 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Zinc on D | UNIMOD:954 | 1 |
| Zinc on E | UNIMOD:954 | 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
319e7d516631aaa0, written 2026-10-29T11:20:58+00:00 by ingester 1.4.0- Reconciliation
- failed: peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group