Generated summary
PXD015239 is a DDA label-free dataset (Homo sapiens) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 229,035 PSMs, 21,719 peptidoforms and 2,140 protein groups, and the repository holds 8,495 PTM sites for it. 5 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, 5 warnings and 1 for information
count_mismatch warning
The bundle holds 229035 where the producer reported 229040 (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 229035 where the producer reported 229040 (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
1.69% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
1.69% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
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 30421 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3963 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 30421 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3963 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: 817 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: 817 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
47 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
47 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 | 229,035 |
| Peptidoforms at 1% FDR | 21,719 |
| Protein groups at 1% FDR | 2,140 |
| PTM sites | 8,495 |
| Quantitative values | 194,367 |
| PSMs, all (including decoys and sub-threshold) | 429,985 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 46.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.3% |
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
- none
- Instrument vendor
- not recorded
- Runs / samples
- 10 / 10
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 6ea39b9e1b3a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Deamidation on N | UNIMOD:7 | 1,677 |
| Deamidation on Q | UNIMOD:7 | 1,416 |
| Oxidation on M | UNIMOD:35 | 715 |
| Citrullination on R | UNIMOD:7 | 483 |
| Hydroxylation on P | UNIMOD:35 | 290 |
| Ammonia loss on N | UNIMOD:385 | 284 |
| Fe[II] on E | UNIMOD:952 | 215 |
| Fe[II] on D | UNIMOD:952 | 187 |
| Fe[III] on E | UNIMOD:1870 | 160 |
| Magnesium on D | UNIMOD:956 | 159 |
| N-acetylalanine on A | UNIMOD:1 | 159 |
| Magnesium on E | UNIMOD:956 | 158 |
| Fe[III] on D | UNIMOD:1870 | 145 |
| Sodium on E | UNIMOD:30 | 145 |
| Sodium on D | UNIMOD:30 | 142 |
| Calcium on D | UNIMOD:951 | 127 |
| Calcium on E | UNIMOD:951 | 125 |
| Hydroxylation on K | UNIMOD:35 | 125 |
| Hydroxylation on N | UNIMOD:35 | 122 |
| Phosphoserine on S | UNIMOD:21 | 113 |
| Acetylation on X | UNIMOD:1 | 78 |
| Phosphorylation on S | UNIMOD:21 | 75 |
| Methylation on K | UNIMOD:34 | 70 |
| N-acetylmethionine on M | UNIMOD:1 | 70 |
| Carbamyl on X | UNIMOD:5 | 69 |
| N-acetylserine on S | UNIMOD:1 | 64 |
| Phosphorylation on T | UNIMOD:21 | 58 |
| Potassium on D | UNIMOD:530 | 51 |
| Potassium on E | UNIMOD:530 | 46 |
| Water Loss on E | UNIMOD:27 | 42 |
| Formylation on K | UNIMOD:122 | 41 |
| Methylation on R | UNIMOD:34 | 38 |
| Acetylation on K | UNIMOD:1 | 37 |
| Dimethylation on K | UNIMOD:36 | 34 |
| N6-acetyllysine on K | UNIMOD:1 | 31 |
| Phosphothreonine on T | UNIMOD:21 | 26 |
| Dimethylation on R | UNIMOD:36 | 23 |
| Glutarylation on K | UNIMOD:1848 | 23 |
| Sulfonation on Y | UNIMOD:40 | 23 |
| N-acetylthreonine on T | UNIMOD:1 | 19 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 19 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| Carbamyl on K | UNIMOD:5 | 17 |
| Trimethylation on K | UNIMOD:37 | 17 |
| Crotonylation on K | UNIMOD:1363 | 14 |
| Cu[I] on E | UNIMOD:531 | 14 |
| Omega-N-methylarginine on R | UNIMOD:34 | 14 |
| Carboxylation on D | UNIMOD:299 | 13 |
| Carboxylation on E | UNIMOD:299 | 13 |
| Hydroxybutyrylation on K | — | 13 |
| N-myristoyl glycine on G | UNIMOD:45 | 13 |
| Citrulline on R | UNIMOD:7 | 12 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 12 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 11 |
| Succinylation on K | UNIMOD:64 | 10 |
| HexNAc on S | UNIMOD:43 | 9 |
| N6-succinyllysine on K | — | 9 |
| Nitrosylation on C | UNIMOD:275 | 9 |
| Phosphorylation on Y | UNIMOD:21 | 9 |
| Ammonia loss on C | UNIMOD:385 | 8 |
| Butyrylation on K | UNIMOD:1289 | 8 |
| HexNAc on T | UNIMOD:43 | 8 |
| N-acetylvaline on V | UNIMOD:1 | 8 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| Carbamyl on R | UNIMOD:5 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| Nitrosylation on Y | UNIMOD:354 | 7 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| Carbamyl on M | UNIMOD:5 | 6 |
| Carboxylation on K | UNIMOD:299 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| Cu[I] on D | UNIMOD:531 | 5 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 5 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carbamyl on C | UNIMOD:5 | 3 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| N6-methyllysine on K | UNIMOD:34 | 3 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| Cysteine methyl ester on C | UNIMOD:34 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-pyruvate 2-iminyl-valine on V | UNIMOD:422 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| N6-malonyllysine on K | — | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-glutathionyl cysteine on C | UNIMOD:55 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
5deec457676bdd22, written 2026-10-29T09:10:09+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