Generated summary
PXD023381 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 42,734 PSMs, 9,844 peptidoforms and 1,278 protein groups, and the repository holds 5,335 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 2 for information
count_mismatch warning
The bundle holds 42734 where the producer reported 42742 (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 42734 where the producer reported 42742 (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
62.10% of protein intensity in the worst file, 18.25% median across 20 files (DEF-QC-9 v3.5)
62.10% of protein intensity in the worst file, 18.25% median across 20 files (DEF-QC-9 v3.5)
low_core_use warning
10.87 avg cores of 32 allowed (S5)
10.87 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 8768 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 490 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 8768 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 490 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: 47 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: 47 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.
collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD023381:P13928;Q5VT79 written 2 times; quant_values: 20 identifier(s), 20 row(s) dropped, e.g. PXD023381:MSB40881Band_01:label_free:protein_group:PXD023381:P13928;Q5VT79:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD023381:P13928;Q5VT79 written 2 times; quant_values: 20 identifier(s), 20 row(s) dropped, e.g. PXD023381:MSB40881Band_01:label_free:protein_group:PXD023381:P13928;Q5VT79:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
10 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
10 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 | 42,734 |
| Peptidoforms at 1% FDR | 9,844 |
| Protein groups at 1% FDR | 1,278 |
| PTM sites | 5,335 |
| Quantitative values | 107,530 |
| PSMs, all (including decoys and sub-threshold) | 94,485 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 35.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 16.3% |
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
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 1,711 |
| Carbamidomethyl on C | UNIMOD:4 | 1,590 |
| Deamidation on N | UNIMOD:7 | 244 |
| Hydroxylation on P | UNIMOD:35 | 204 |
| Deamidation on Q | UNIMOD:7 | 97 |
| Hydroxylation on N | UNIMOD:35 | 95 |
| Hydroxylation on K | UNIMOD:35 | 70 |
| Sodium on D | UNIMOD:30 | 69 |
| Sodium on E | UNIMOD:30 | 68 |
| N-acetylalanine on A | UNIMOD:1 | 54 |
| Fe[II] on D | UNIMOD:952 | 41 |
| Ammonia loss on N | UNIMOD:385 | 39 |
| Fe[II] on E | UNIMOD:952 | 26 |
| Calcium on D | UNIMOD:951 | 25 |
| Methylation on K | UNIMOD:34 | 24 |
| Phosphoserine on S | UNIMOD:21 | 22 |
| Fe[III] on E | UNIMOD:1870 | 21 |
| Ammonia loss on C | UNIMOD:385 | 20 |
| Formylation on K | UNIMOD:122 | 20 |
| Magnesium on D | UNIMOD:956 | 20 |
| Magnesium on E | UNIMOD:956 | 20 |
| N-acetylserine on S | UNIMOD:1 | 19 |
| Fe[III] on D | UNIMOD:1870 | 18 |
| N6-acetyllysine on K | UNIMOD:1 | 18 |
| Calcium on E | UNIMOD:951 | 16 |
| Carbamyl on X | UNIMOD:5 | 16 |
| Methylation on R | UNIMOD:34 | 15 |
| Citrullination on R | UNIMOD:7 | 14 |
| Deamidated asparagine on N | UNIMOD:7 | 14 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 14 |
| Acetylation on K | UNIMOD:1 | 13 |
| Dimethylation on K | UNIMOD:36 | 12 |
| Water Loss on E | UNIMOD:27 | 12 |
| Hydroxyproline on P | UNIMOD:35 | 11 |
| N-acetylmethionine on M | UNIMOD:1 | 11 |
| Carbamyl on M | UNIMOD:5 | 10 |
| Phosphorylation on S | UNIMOD:21 | 10 |
| N6-methyllysine on K | UNIMOD:34 | 9 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 7 |
| N6-glutaryllysine on K | — | 7 |
| Potassium on E | UNIMOD:530 | 7 |
| Acetylation on X | UNIMOD:1 | 6 |
| N-acetylthreonine on T | UNIMOD:1 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 5 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 4 |
| 4-hydroxyproline on P | UNIMOD:35 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Phosphorylation on T | UNIMOD:21 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Dimethylation on R | UNIMOD:36 | 2 |
| HexNAc on S | UNIMOD:43 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N6-crotonyllysine on K | — | 2 |
| Nitrosylation on Y | UNIMOD:354 | 2 |
| Potassium on D | UNIMOD:530 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| Carbamyl on R | UNIMOD:5 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-methacryllysine on K | — | 1 |
| Phosphothreonine on T | UNIMOD:21 | 1 |
| Tele-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
4719624a5135112c, written 2026-10-29T09:49:03+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