Generated summary
PXD006589 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 546,673 PSMs, 54,505 peptidoforms and 5,244 protein groups, and the repository holds 27,252 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 546673 where the producer reported 546682 (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 546673 where the producer reported 546682 (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.
low_core_use warning
15.87 avg cores of 32 allowed (S5)
15.87 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 236981 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10298 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 236981 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10298 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
906 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 3004 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. `AAAAAAAGDSDS[UniProt:Phosphoserine on S]WDADAFSVEDPVRK|AAAAAAAGDS[UniProt:Phosphoserine on S]DSWDADAFSVEDPVRK`, `AAAGELQED[Metal:Calcium on D]SGLC[Common Fixed:Carbamidomethyl on C]VLAR|AAAGELQE[Metal:Calcium on E]DSGLC[Common Fixed:Carbamidomethyl on C]VLAR|AAAGE[Metal:Calcium on E]LQEDSGLC[Common Fixed:Carbamidomethyl on C]VLAR`, `AAAMLPTVGEGYGYGPE[Metal:Sodium on E]SELSQASAATR|AAAMLPTVGE[Metal:Sodium on E]GYGYGPESELSQASAATR`.
906 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 3004 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. `AAAAAAAGDSDS[UniProt:Phosphoserine on S]WDADAFSVEDPVRK|AAAAAAAGDS[UniProt:Phosphoserine on S]DSWDADAFSVEDPVRK`, `AAAGELQED[Metal:Calcium on D]SGLC[Common Fixed:Carbamidomethyl on C]VLAR|AAAGELQE[Metal:Calcium on E]DSGLC[Common Fixed:Carbamidomethyl on C]VLAR|AAAGE[Metal:Calcium on E]LQEDSGLC[Common Fixed:Carbamidomethyl on C]VLAR`, `AAAMLPTVGEGYGYGPE[Metal:Sodium on E]SELSQASAATR|AAAMLPTVGE[Metal:Sodium on E]GYGYGPESELSQASAATR`.
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: 1149 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: 1149 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
50 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
50 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 | 546,673 |
| Peptidoforms at 1% FDR | 54,505 |
| Protein groups at 1% FDR | 5,244 |
| PTM sites | 27,252 |
| Quantitative values | 606,497 |
| PSMs, all (including decoys and sub-threshold) | 860,662 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 73.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.5% |
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 | 10,259 |
| Oxidation on M | UNIMOD:35 | 2,825 |
| Deamidation on N | UNIMOD:7 | 2,309 |
| Sodium on E | UNIMOD:30 | 1,155 |
| Calcium on E | UNIMOD:951 | 957 |
| Sodium on D | UNIMOD:30 | 949 |
| Magnesium on E | UNIMOD:956 | 923 |
| Phosphoserine on S | UNIMOD:21 | 873 |
| Deamidation on Q | UNIMOD:7 | 802 |
| Calcium on D | UNIMOD:951 | 797 |
| Magnesium on D | UNIMOD:956 | 753 |
| Ammonia loss on C | UNIMOD:385 | 619 |
| Ammonia loss on N | UNIMOD:385 | 454 |
| N-acetylalanine on A | UNIMOD:1 | 324 |
| N-acetylmethionine on M | UNIMOD:1 | 202 |
| Acetylation on X | UNIMOD:1 | 198 |
| Potassium on D | UNIMOD:530 | 183 |
| Potassium on E | UNIMOD:530 | 177 |
| Citrullination on R | UNIMOD:7 | 147 |
| Phosphothreonine on T | UNIMOD:21 | 142 |
| Phosphorylation on S | UNIMOD:21 | 138 |
| N-acetylserine on S | UNIMOD:1 | 136 |
| Carbamyl on X | UNIMOD:5 | 105 |
| Hydroxylation on P | UNIMOD:35 | 102 |
| Water Loss on E | UNIMOD:27 | 95 |
| Fe[III] on E | UNIMOD:1870 | 90 |
| Hydroxylation on N | UNIMOD:35 | 86 |
| N6-acetyllysine on K | UNIMOD:1 | 83 |
| Phosphorylation on T | UNIMOD:21 | 83 |
| Fe[III] on D | UNIMOD:1870 | 77 |
| Acetylation on K | UNIMOD:1 | 71 |
| Methylation on K | UNIMOD:34 | 62 |
| Carbamyl on K | UNIMOD:5 | 54 |
| Omega-N-methylarginine on R | UNIMOD:34 | 42 |
| Hydroxylation on K | UNIMOD:35 | 41 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 34 |
| N6-glutaryllysine on K | — | 33 |
| Carbamyl on M | UNIMOD:5 | 32 |
| HexNAc on T | UNIMOD:43 | 32 |
| Methylation on R | UNIMOD:34 | 30 |
| Phosphotyrosine on Y | UNIMOD:21 | 29 |
| 4-hydroxyproline on P | UNIMOD:35 | 28 |
| Formylation on K | UNIMOD:122 | 28 |
| HexNAc on S | UNIMOD:43 | 27 |
| Phosphorylation on Y | UNIMOD:21 | 25 |
| Dimethylation on R | UNIMOD:36 | 24 |
| Dimethylation on K | UNIMOD:36 | 23 |
| N-acetylthreonine on T | UNIMOD:1 | 23 |
| Fe[II] on D | UNIMOD:952 | 21 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 20 |
| Deamidated asparagine on N | UNIMOD:7 | 18 |
| Cu[I] on D | UNIMOD:531 | 17 |
| Glutarylation on K | UNIMOD:1848 | 16 |
| Fe[II] on E | UNIMOD:952 | 15 |
| Malonylation on K | UNIMOD:747 | 15 |
| Zinc on D | UNIMOD:954 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| Trimethylation on K | UNIMOD:37 | 12 |
| Carboxylation on D | UNIMOD:299 | 10 |
| N5-methylglutamine on Q | UNIMOD:34 | 10 |
| N6-succinyllysine on K | — | 10 |
| Succinylation on K | UNIMOD:64 | 10 |
| Carboxylation on E | UNIMOD:299 | 9 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 9 |
| N6-crotonyllysine on K | — | 9 |
| Citrulline on R | UNIMOD:7 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 8 |
| Cu[I] on E | UNIMOD:531 | 7 |
| Zinc on E | UNIMOD:954 | 7 |
| Butyrylation on K | UNIMOD:1289 | 6 |
| Hydroxybutyrylation on K | — | 6 |
| Hydroxyproline on P | UNIMOD:35 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 5 |
| Allysine on K | UNIMOD:352 | 4 |
| Carbamyl on R | UNIMOD:5 | 4 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| N6-propionyllysine on K | UNIMOD:58 | 4 |
| Nitrosylation on C | UNIMOD:275 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carbamyl on C | UNIMOD:5 | 3 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N6-methacryllysine on K | — | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| Sulfonation on Y | UNIMOD:40 | 1 |
| Sulfotyrosine on Y | UNIMOD:40 | 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
89ff40bd1316f31d, written 2026-11-01T18:44:56+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