Generated summary
PXD013240 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 132,407 PSMs, 16,738 peptidoforms and 2,806 protein groups, and the repository holds 9,315 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 1 for information
high_contamination warning
63.70% of protein intensity in the worst file, 4.41% median across 16 files (DEF-QC-9 v3.5)
63.70% of protein intensity in the worst file, 4.41% median across 16 files (DEF-QC-9 v3.5)
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 25287 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4945 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 25287 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4945 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: 308 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: 308 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
9 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
9 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 | 132,407 |
| Peptidoforms at 1% FDR | 16,738 |
| Protein groups at 1% FDR | 2,806 |
| PTM sites | 9,315 |
| Quantitative values | 277,893 |
| PSMs, all (including decoys and sub-threshold) | 294,282 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 17.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 5.1% |
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
- none
- Instrument vendor
- not recorded
- Runs / samples
- 16 / 16
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 3,649 |
| Deamidation on N | UNIMOD:7 | 702 |
| Deamidation on Q | UNIMOD:7 | 620 |
| Sodium on E | UNIMOD:30 | 308 |
| Oxidation on M | UNIMOD:35 | 282 |
| Sodium on D | UNIMOD:30 | 275 |
| N-acetylalanine on A | UNIMOD:1 | 261 |
| Magnesium on E | UNIMOD:956 | 214 |
| Magnesium on D | UNIMOD:956 | 178 |
| Hydroxylation on P | UNIMOD:35 | 169 |
| Carbamyl on M | UNIMOD:5 | 148 |
| Ammonia loss on N | UNIMOD:385 | 142 |
| Calcium on E | UNIMOD:951 | 133 |
| Phosphoserine on S | UNIMOD:21 | 133 |
| Calcium on D | UNIMOD:951 | 111 |
| Acetylation on K | UNIMOD:1 | 91 |
| Methylation on K | UNIMOD:34 | 91 |
| Carbamyl on X | UNIMOD:5 | 86 |
| Trimethylation on K | UNIMOD:37 | 85 |
| Citrullination on R | UNIMOD:7 | 78 |
| Ammonia loss on C | UNIMOD:385 | 77 |
| N-acetylserine on S | UNIMOD:1 | 69 |
| Phosphorylation on S | UNIMOD:21 | 60 |
| Acetylation on X | UNIMOD:1 | 46 |
| Methylation on R | UNIMOD:34 | 42 |
| N-acetylmethionine on M | UNIMOD:1 | 42 |
| N6-acetyllysine on K | UNIMOD:1 | 36 |
| Phosphorylation on T | UNIMOD:21 | 31 |
| 4-hydroxyproline on P | UNIMOD:35 | 28 |
| Carbamyl on K | UNIMOD:5 | 25 |
| Fe[II] on D | UNIMOD:952 | 25 |
| Carboxylation on D | UNIMOD:299 | 23 |
| Carboxylation on E | UNIMOD:299 | 22 |
| Dimethylation on K | UNIMOD:36 | 22 |
| Glutarylation on K | UNIMOD:1848 | 22 |
| Hydroxylation on K | UNIMOD:35 | 22 |
| Hydroxylation on N | UNIMOD:35 | 22 |
| Fe[II] on E | UNIMOD:952 | 21 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 20 |
| N-acetylthreonine on T | UNIMOD:1 | 20 |
| Potassium on D | UNIMOD:530 | 19 |
| Potassium on E | UNIMOD:530 | 17 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 14 |
| Phosphothreonine on T | UNIMOD:21 | 14 |
| Carbamyl on R | UNIMOD:5 | 13 |
| Carboxylation on K | UNIMOD:299 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 13 |
| Water Loss on E | UNIMOD:27 | 13 |
| Dimethylation on R | UNIMOD:36 | 12 |
| Butyrylation on K | UNIMOD:1289 | 11 |
| Formylation on K | UNIMOD:122 | 11 |
| Hydroxybutyrylation on K | — | 10 |
| Fe[III] on D | UNIMOD:1870 | 9 |
| HexNAc on S | UNIMOD:43 | 9 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 8 |
| Malonylation on K | UNIMOD:747 | 8 |
| Omega-N-methylarginine on R | UNIMOD:34 | 8 |
| Sulfonation on Y | UNIMOD:40 | 8 |
| Carbamyl on C | UNIMOD:5 | 7 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| Fe[III] on E | UNIMOD:1870 | 6 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| Crotonylation on K | UNIMOD:1363 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| HexNAc on T | UNIMOD:43 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| Nitrosylation on C | UNIMOD:275 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| Nitrosylation on Y | UNIMOD:354 | 3 |
| Phosphorylation on Y | UNIMOD:21 | 3 |
| Citrulline on R | UNIMOD:7 | 2 |
| N6-glutaryllysine on K | — | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 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
a21e4f11590eb3b0, written 2026-10-29T09:31:24+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