Generated summary
PXD006578 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 671,443 PSMs, 69,065 peptidoforms and 6,127 protein groups, and the repository holds 33,985 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 671443 where the producer reported 671456 (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 671443 where the producer reported 671456 (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
7.57% of protein intensity in the worst file, 3.09% median across 18 files (DEF-QC-9 v3.5)
7.57% of protein intensity in the worst file, 3.09% median across 18 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 299062 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 14818 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 299062 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 14818 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).
peptide_rows_localization_ambiguous warning
1241 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 3539 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAAAAAAAAPAAAATAPTTAATT[Common Biological:HexNAc on T]AATAAQ|AAAAAAAAAPAAAATAPTTAAT[Common Biological:HexNAc on T]TAATAAQ`, `AAAEVNQ[Common Artifact:Deamidation on Q]DYGLDPK|AAAEVN[Common Artifact:Deamidation on N]QDYGLDPK`, `AAAGAPDGMEEPGM[Common Variable:Oxidation on M]DTEAETVATEAPAR[Common Biological:Dimethylation on R]PVNC[Common Fixed:Carbamidomethyl on C]LEAEAAAGAAAEDSGAAR|AAAGAPDGM[Common Variable:Oxidation on M]EEPGMDTEAETVATEAPAR[Common Biological:Dimethylation on R]PVNC[Common Fixed:Carbamidomethyl on C]LEAEAAAGAAAEDSGAAR`.
1241 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 3539 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAAAAAAAAPAAAATAPTTAATT[Common Biological:HexNAc on T]AATAAQ|AAAAAAAAAPAAAATAPTTAAT[Common Biological:HexNAc on T]TAATAAQ`, `AAAEVNQ[Common Artifact:Deamidation on Q]DYGLDPK|AAAEVN[Common Artifact:Deamidation on N]QDYGLDPK`, `AAAGAPDGMEEPGM[Common Variable:Oxidation on M]DTEAETVATEAPAR[Common Biological:Dimethylation on R]PVNC[Common Fixed:Carbamidomethyl on C]LEAEAAAGAAAEDSGAAR|AAAGAPDGM[Common Variable:Oxidation on M]EEPGMDTEAETVATEAPAR[Common Biological:Dimethylation on R]PVNC[Common Fixed:Carbamidomethyl on C]LEAEAAAGAAAEDSGAAR`.
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: 2056 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: 2056 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
48 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
48 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 | 671,443 |
| Peptidoforms at 1% FDR | 69,065 |
| Protein groups at 1% FDR | 6,127 |
| PTM sites | 33,985 |
| Quantitative values | 738,096 |
| PSMs, all (including decoys and sub-threshold) | 1,141,899 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 77.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.7% |
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
- 18 / 18
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v6.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 12,856 |
| Oxidation on M | UNIMOD:35 | 3,596 |
| Deamidation on N | UNIMOD:7 | 2,844 |
| Sodium on E | UNIMOD:30 | 1,348 |
| Calcium on E | UNIMOD:951 | 1,239 |
| Magnesium on E | UNIMOD:956 | 1,186 |
| Sodium on D | UNIMOD:30 | 1,086 |
| Calcium on D | UNIMOD:951 | 1,033 |
| Deamidation on Q | UNIMOD:7 | 946 |
| Magnesium on D | UNIMOD:956 | 884 |
| Phosphoserine on S | UNIMOD:21 | 821 |
| Ammonia loss on C | UNIMOD:385 | 668 |
| Ammonia loss on N | UNIMOD:385 | 469 |
| N-acetylalanine on A | UNIMOD:1 | 453 |
| N-acetylmethionine on M | UNIMOD:1 | 283 |
| Acetylation on X | UNIMOD:1 | 281 |
| Potassium on E | UNIMOD:530 | 263 |
| Carbamyl on X | UNIMOD:5 | 215 |
| Potassium on D | UNIMOD:530 | 201 |
| N-acetylserine on S | UNIMOD:1 | 171 |
| N6-acetyllysine on K | UNIMOD:1 | 163 |
| Citrullination on R | UNIMOD:7 | 160 |
| Phosphothreonine on T | UNIMOD:21 | 128 |
| Methylation on K | UNIMOD:34 | 122 |
| Hydroxylation on P | UNIMOD:35 | 113 |
| Water Loss on E | UNIMOD:27 | 105 |
| Fe[III] on D | UNIMOD:1870 | 99 |
| Fe[III] on E | UNIMOD:1870 | 96 |
| Phosphorylation on S | UNIMOD:21 | 93 |
| Acetylation on K | UNIMOD:1 | 86 |
| Hydroxylation on N | UNIMOD:35 | 77 |
| Phosphorylation on T | UNIMOD:21 | 69 |
| Carbamyl on K | UNIMOD:5 | 68 |
| Methylation on R | UNIMOD:34 | 59 |
| Carbamyl on M | UNIMOD:5 | 47 |
| Trimethylation on K | UNIMOD:37 | 44 |
| Hydroxylation on K | UNIMOD:35 | 41 |
| Dimethylation on K | UNIMOD:36 | 37 |
| N-acetylthreonine on T | UNIMOD:1 | 37 |
| N6-succinyllysine on K | — | 36 |
| Fe[II] on D | UNIMOD:952 | 33 |
| HexNAc on T | UNIMOD:43 | 31 |
| Dimethylation on R | UNIMOD:36 | 29 |
| Phosphotyrosine on Y | UNIMOD:21 | 28 |
| Malonylation on K | UNIMOD:747 | 27 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 26 |
| Fe[II] on E | UNIMOD:952 | 23 |
| HexNAc on S | UNIMOD:43 | 22 |
| Omega-N-methylarginine on R | UNIMOD:34 | 22 |
| Formylation on K | UNIMOD:122 | 21 |
| 4-hydroxyproline on P | UNIMOD:35 | 19 |
| Butyrylation on K | UNIMOD:1289 | 19 |
| Glutarylation on K | UNIMOD:1848 | 17 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| Hydroxybutyrylation on K | — | 14 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Carboxylation on D | UNIMOD:299 | 13 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 12 |
| Carboxylation on E | UNIMOD:299 | 12 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| Phosphorylation on Y | UNIMOD:21 | 12 |
| N-acetylglycine on G | UNIMOD:1 | 11 |
| Succinylation on K | UNIMOD:64 | 11 |
| Cu[I] on D | UNIMOD:531 | 10 |
| Carbamyl on R | UNIMOD:5 | 9 |
| Citrulline on R | UNIMOD:7 | 9 |
| Nitrosylation on Y | UNIMOD:354 | 9 |
| Zinc on D | UNIMOD:954 | 9 |
| Crotonylation on K | UNIMOD:1363 | 8 |
| Cu[I] on E | UNIMOD:531 | 8 |
| N-acetylvaline on V | UNIMOD:1 | 8 |
| N6-butyryllysine on K | UNIMOD:1289 | 8 |
| Zinc on E | UNIMOD:954 | 8 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 7 |
| Carbamyl on C | UNIMOD:5 | 6 |
| Carboxylation on K | UNIMOD:299 | 6 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| Allysine on K | UNIMOD:352 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Nitrosylation on C | UNIMOD:275 | 4 |
| Hydroxyproline on P | UNIMOD:35 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| N6-crotonyllysine on K | — | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfenic acid (-SOH) on C | UNIMOD:35 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Glu to PyroGlu on Q | UNIMOD:28 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| Sulfonation on Y | UNIMOD:40 | 1 |
| Sulfoserine on S | UNIMOD:40 | 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
17c2c2f917127598, written 2026-11-01T23:32:01+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