Generated summary
PXD050351 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and enrichment: chemical_probe. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 213,526 PSMs, 15,770 peptidoforms and 1,481 protein groups, and the repository holds 7,765 PTM sites for it. 4 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, 4 warnings and 2 for information
low_core_use warning
15.17 avg cores of 32 allowed (S5)
15.17 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 24647 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2671 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 24647 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2671 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: 1140 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: 1140 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD050351:O75122;Q7Z460 written 2 times; quant_values: 40 identifier(s), 40 row(s) dropped, e.g. PXD050351:03189_GA1_P036513_B00_A00_R1:label_free:protein_group:PXD050351:O75122;Q7Z460: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: 2 identifier(s), 2 row(s) dropped, e.g. PXD050351:O75122;Q7Z460 written 2 times; quant_values: 40 identifier(s), 40 row(s) dropped, e.g. PXD050351:03189_GA1_P036513_B00_A00_R1:label_free:protein_group:PXD050351:O75122;Q7Z460:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
21 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
21 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 | 213,526 |
| Peptidoforms at 1% FDR | 15,770 |
| Protein groups at 1% FDR | 1,481 |
| PTM sites | 7,765 |
| Quantitative values | 334,292 |
| PSMs, all (including decoys and sub-threshold) | 304,565 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 60.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.4% |
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
- chemical_probe
- 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 | 2,462 |
| Carbamidomethyl on C | UNIMOD:4 | 2,124 |
| Hydroxylation on P | UNIMOD:35 | 386 |
| Acetylation on K | UNIMOD:1 | 308 |
| Deamidation on N | UNIMOD:7 | 277 |
| Hydroxylation on N | UNIMOD:35 | 255 |
| Deamidation on Q | UNIMOD:7 | 218 |
| Hydroxylation on K | UNIMOD:35 | 142 |
| Phosphoserine on S | UNIMOD:21 | 137 |
| Carbamyl on X | UNIMOD:5 | 118 |
| Fe[III] on E | UNIMOD:1870 | 112 |
| Fe[III] on D | UNIMOD:1870 | 99 |
| N-acetylalanine on A | UNIMOD:1 | 88 |
| Phosphorylation on S | UNIMOD:21 | 83 |
| Citrullination on R | UNIMOD:7 | 55 |
| N-acetylserine on S | UNIMOD:1 | 49 |
| Phosphorylation on T | UNIMOD:21 | 49 |
| Acetylation on X | UNIMOD:1 | 46 |
| Methylation on K | UNIMOD:34 | 37 |
| Phosphothreonine on T | UNIMOD:21 | 35 |
| Ammonia loss on N | UNIMOD:385 | 32 |
| N-acetylmethionine on M | UNIMOD:1 | 32 |
| N6-acetyllysine on K | UNIMOD:1 | 25 |
| Phosphotyrosine on Y | UNIMOD:21 | 25 |
| Sulfonation on Y | UNIMOD:40 | 25 |
| Formylation on K | UNIMOD:122 | 22 |
| Carbamyl on K | UNIMOD:5 | 19 |
| Methylation on R | UNIMOD:34 | 19 |
| Fe[II] on E | UNIMOD:952 | 17 |
| Fe[II] on D | UNIMOD:952 | 15 |
| HexNAc on S | UNIMOD:43 | 15 |
| Ammonia loss on C | UNIMOD:385 | 14 |
| Trimethylation on K | UNIMOD:37 | 13 |
| Phosphorylation on Y | UNIMOD:21 | 11 |
| N6-glutaryllysine on K | — | 10 |
| Dimethylation on K | UNIMOD:36 | 9 |
| Dimethylation on R | UNIMOD:36 | 9 |
| Magnesium on E | UNIMOD:956 | 9 |
| N-acetylthreonine on T | UNIMOD:1 | 9 |
| Water Loss on E | UNIMOD:27 | 9 |
| Carbamyl on R | UNIMOD:5 | 8 |
| Malonylation on K | UNIMOD:747 | 8 |
| Sodium on E | UNIMOD:30 | 8 |
| Carbamyl on M | UNIMOD:5 | 7 |
| Magnesium on D | UNIMOD:956 | 7 |
| Sodium on D | UNIMOD:30 | 7 |
| HexNAc on T | UNIMOD:43 | 6 |
| 4-hydroxyproline on P | UNIMOD:35 | 5 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 5 |
| Carboxylation on E | UNIMOD:299 | 5 |
| Carboxylation on K | UNIMOD:299 | 5 |
| N6-methyllysine on K | UNIMOD:34 | 5 |
| Omega-N-methylarginine on R | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Butyrylation on K | UNIMOD:1289 | 4 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 4 |
| N6-succinyllysine on K | — | 4 |
| Hydroxybutyrylation on K | — | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 3 |
| Calcium on E | UNIMOD:951 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Carboxylation on D | UNIMOD:299 | 2 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| Potassium on E | 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
965b5e82e9853696, written 2026-10-29T09:28:46+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