Generated summary
PXD006023 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 767,748 PSMs, 54,669 peptidoforms and 5,347 protein groups, and the repository holds 13,244 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 767748 where the producer reported 767751 (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 767748 where the producer reported 767751 (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
10.46 avg cores of 32 allowed (S5)
10.46 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 69055 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10010 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 69055 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10010 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
207 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 739 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. `AAFDD[Metal:Fe[III] on D]AIAELDTLSEESYK|AAFD[Metal:Fe[III] on D]DAIAELDTLSEESYK`, `AFADALEVIPMALSENSGM[Common Variable:Oxidation on M]NPIQTMTEVR|AFADALEVIPM[Common Variable:Oxidation on M]ALSENSGMNPIQTMTEVR`, `AIQAYGMKPHDIFEANDLFENGNM[Common Variable:Oxidation on M]TQVQTTLVALAGLAK|AIQAYGM[Common Variable:Oxidation on M]KPHDIFEANDLFENGNMTQVQTTLVALAGLAK`.
207 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 739 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. `AAFDD[Metal:Fe[III] on D]AIAELDTLSEESYK|AAFD[Metal:Fe[III] on D]DAIAELDTLSEESYK`, `AFADALEVIPMALSENSGM[Common Variable:Oxidation on M]NPIQTMTEVR|AFADALEVIPM[Common Variable:Oxidation on M]ALSENSGMNPIQTMTEVR`, `AIQAYGMKPHDIFEANDLFENGNM[Common Variable:Oxidation on M]TQVQTTLVALAGLAK|AIQAYGM[Common Variable:Oxidation on M]KPHDIFEANDLFENGNMTQVQTTLVALAGLAK`.
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: 659 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: 659 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
59 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
59 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 | 767,748 |
| Peptidoforms at 1% FDR | 54,669 |
| Protein groups at 1% FDR | 5,347 |
| PTM sites | 13,244 |
| Quantitative values | 762,687 |
| PSMs, all (including decoys and sub-threshold) | 1,409,658 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 47.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.1% |
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
- other
- 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 | 6,687 |
| Oxidation on M | UNIMOD:35 | 2,510 |
| Deamidation on N | UNIMOD:7 | 487 |
| N-acetylalanine on A | UNIMOD:1 | 322 |
| Ammonia loss on N | UNIMOD:385 | 293 |
| N-acetylmethionine on M | UNIMOD:1 | 193 |
| Deamidation on Q | UNIMOD:7 | 188 |
| Ammonia loss on C | UNIMOD:385 | 171 |
| Phosphoserine on S | UNIMOD:21 | 150 |
| Sodium on E | UNIMOD:30 | 149 |
| Acetylation on X | UNIMOD:1 | 141 |
| N-acetylserine on S | UNIMOD:1 | 128 |
| Carbamyl on X | UNIMOD:5 | 112 |
| Sodium on D | UNIMOD:30 | 112 |
| Water Loss on E | UNIMOD:27 | 73 |
| Magnesium on D | UNIMOD:956 | 65 |
| N6-acetyllysine on K | UNIMOD:1 | 64 |
| Hydroxylation on P | UNIMOD:35 | 58 |
| Magnesium on E | UNIMOD:956 | 58 |
| Methylation on K | UNIMOD:34 | 48 |
| Calcium on D | UNIMOD:951 | 46 |
| Omega-N-methylarginine on R | UNIMOD:34 | 41 |
| Citrullination on R | UNIMOD:7 | 40 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 39 |
| Dimethylation on R | UNIMOD:36 | 38 |
| Calcium on E | UNIMOD:951 | 36 |
| Phosphorylation on S | UNIMOD:21 | 36 |
| Fe[III] on D | UNIMOD:1870 | 35 |
| Phosphothreonine on T | UNIMOD:21 | 30 |
| N6-methyllysine on K | UNIMOD:34 | 29 |
| Hydroxylation on N | UNIMOD:35 | 26 |
| N-acetylthreonine on T | UNIMOD:1 | 26 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 25 |
| Phosphorylation on T | UNIMOD:21 | 25 |
| Methylation on R | UNIMOD:34 | 24 |
| Dimethylation on K | UNIMOD:36 | 23 |
| Fe[III] on E | UNIMOD:1870 | 23 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 23 |
| Acetylation on K | UNIMOD:1 | 22 |
| HexNAc on T | UNIMOD:43 | 19 |
| Potassium on D | UNIMOD:530 | 15 |
| N6-glutaryllysine on K | — | 14 |
| HexNAc on S | UNIMOD:43 | 11 |
| Hydroxylation on K | UNIMOD:35 | 11 |
| Fe[II] on D | UNIMOD:952 | 10 |
| Fe[II] on E | UNIMOD:952 | 10 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 10 |
| Malonylation on K | UNIMOD:747 | 10 |
| Phosphotyrosine on Y | UNIMOD:21 | 10 |
| N-myristoyl glycine on G | UNIMOD:45 | 9 |
| Glutarylation on K | UNIMOD:1848 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| Phosphorylation on Y | UNIMOD:21 | 8 |
| Trimethylation on K | UNIMOD:37 | 8 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 7 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| N6-succinyllysine on K | — | 6 |
| 5-glutamyl serotonin on Q | — | 5 |
| Allysine on K | UNIMOD:352 | 5 |
| Formylation on K | UNIMOD:122 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-butyryllysine on K | UNIMOD:1289 | 5 |
| Succinylation on K | UNIMOD:64 | 5 |
| Butyrylation on K | UNIMOD:1289 | 4 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| Hydroxybutyrylation on K | — | 4 |
| Potassium on E | UNIMOD:530 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 4-hydroxyproline on P | UNIMOD:35 | 3 |
| N6-crotonyllysine on K | — | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| N6-lipoyllysine on K | UNIMOD:42 | 2 |
| N6-malonyllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| ADP-ribosyl glutamic acid on E | — | 1 |
| Cu[I] on E | UNIMOD:531 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-methacryllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| Zinc on E | UNIMOD:954 | 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
27adc21840b5405e, written 2026-11-01T11:19:06+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