Generated summary
PXD073999 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 514,178 PSMs, 26,734 peptidoforms and 3,232 protein groups, and the repository holds 15,329 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 514178 where the producer reported 514197 (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 514178 where the producer reported 514197 (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
12.18 avg cores of 32 allowed (S5)
12.18 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 114247 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4908 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 114247 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4908 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
686 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 3256 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. `AAFDDAIAELD[Metal:Potassium on D]TLSEESYKDSTLIMQLLR|AAFDDAIAE[Metal:Potassium on E]LDTLSEESYKDSTLIMQLLR`, `AAFDDAIAELD[Metal:Potassium on D]TLSEESYK[Common Biological:Methylation on K]DSTLIMQLLR|AAFDDAIAE[Metal:Potassium on E]LDTLSEESYK[Common Biological:Methylation on K]DSTLIMQLLR`, `AAFNSGKVDIVAINDPFID[Metal:Potassium on D]LNY[UniProt:Phosphotyrosine on Y]MVYMFQYDSTHGK|AAFNSGKVDIVAIND[Metal:Potassium on D]PFIDLNY[UniProt:Phosphotyrosine on Y]MVYMFQYDSTHGK`.
686 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 3256 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. `AAFDDAIAELD[Metal:Potassium on D]TLSEESYKDSTLIMQLLR|AAFDDAIAE[Metal:Potassium on E]LDTLSEESYKDSTLIMQLLR`, `AAFDDAIAELD[Metal:Potassium on D]TLSEESYK[Common Biological:Methylation on K]DSTLIMQLLR|AAFDDAIAE[Metal:Potassium on E]LDTLSEESYK[Common Biological:Methylation on K]DSTLIMQLLR`, `AAFNSGKVDIVAINDPFID[Metal:Potassium on D]LNY[UniProt:Phosphotyrosine on Y]MVYMFQYDSTHGK|AAFNSGKVDIVAIND[Metal:Potassium on D]PFIDLNY[UniProt:Phosphotyrosine on Y]MVYMFQYDSTHGK`.
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: 4140 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: 4140 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
84 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
84 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 | 514,178 |
| Peptidoforms at 1% FDR | 26,734 |
| Protein groups at 1% FDR | 3,232 |
| PTM sites | 15,329 |
| Quantitative values | 351,871 |
| PSMs, all (including decoys and sub-threshold) | 1,190,983 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 66.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.1% |
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
- 12 / 12
- 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 | 6,553 |
| Deamidation on N | UNIMOD:7 | 1,909 |
| Oxidation on M | UNIMOD:35 | 810 |
| Deamidation on Q | UNIMOD:7 | 613 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 543 |
| Carbamyl on M | UNIMOD:5 | 507 |
| Carbamyl on X | UNIMOD:5 | 356 |
| Glutarylation on K | UNIMOD:1848 | 251 |
| Methylation on K | UNIMOD:34 | 233 |
| N-acetylalanine on A | UNIMOD:1 | 201 |
| Acetylation on K | UNIMOD:1 | 179 |
| Sodium on E | UNIMOD:30 | 156 |
| Phosphoserine on S | UNIMOD:21 | 139 |
| Sodium on D | UNIMOD:30 | 136 |
| Ammonia loss on C | UNIMOD:385 | 117 |
| Calcium on D | UNIMOD:951 | 95 |
| Magnesium on E | UNIMOD:956 | 93 |
| Ammonia loss on N | UNIMOD:385 | 91 |
| N6-acetyllysine on K | UNIMOD:1 | 90 |
| Calcium on E | UNIMOD:951 | 89 |
| Hydroxylation on N | UNIMOD:35 | 83 |
| Trimethylation on K | UNIMOD:37 | 83 |
| Fe[II] on E | UNIMOD:952 | 76 |
| Hydroxylation on P | UNIMOD:35 | 73 |
| Carbamyl on K | UNIMOD:5 | 71 |
| N-acetylserine on S | UNIMOD:1 | 71 |
| Fe[II] on D | UNIMOD:952 | 70 |
| Citrullination on R | UNIMOD:7 | 69 |
| Methylation on R | UNIMOD:34 | 69 |
| Magnesium on D | UNIMOD:956 | 67 |
| Potassium on D | UNIMOD:530 | 67 |
| Potassium on E | UNIMOD:530 | 59 |
| Carboxylation on E | UNIMOD:299 | 56 |
| Fe[III] on E | UNIMOD:1870 | 56 |
| Succinylation on K | UNIMOD:64 | 56 |
| Acetylation on X | UNIMOD:1 | 54 |
| Carboxylation on D | UNIMOD:299 | 54 |
| Fe[III] on D | UNIMOD:1870 | 53 |
| Dimethylation on K | UNIMOD:36 | 48 |
| Phosphorylation on S | UNIMOD:21 | 44 |
| Hydroxylation on K | UNIMOD:35 | 37 |
| Phosphothreonine on T | UNIMOD:21 | 37 |
| Hydroxybutyrylation on K | — | 34 |
| N-acetylmethionine on M | UNIMOD:1 | 34 |
| Butyrylation on K | UNIMOD:1289 | 33 |
| Dimethylation on R | UNIMOD:36 | 32 |
| Malonylation on K | UNIMOD:747 | 32 |
| Phosphorylation on T | UNIMOD:21 | 32 |
| Carbamyl on C | UNIMOD:5 | 29 |
| Nitrosylation on Y | UNIMOD:354 | 28 |
| HexNAc on S | UNIMOD:43 | 27 |
| Carbamyl on R | UNIMOD:5 | 26 |
| N6-methyllysine on K | UNIMOD:34 | 21 |
| Crotonylation on K | UNIMOD:1363 | 19 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 18 |
| N6-succinyllysine on K | — | 18 |
| Omega-N-methylarginine on R | UNIMOD:34 | 18 |
| Carboxylation on K | UNIMOD:299 | 16 |
| Deamidated asparagine on N | UNIMOD:7 | 13 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 13 |
| Formylation on K | UNIMOD:122 | 12 |
| HexNAc on T | UNIMOD:43 | 12 |
| N-myristoyl glycine on G | UNIMOD:45 | 11 |
| 4-hydroxyproline on P | UNIMOD:35 | 10 |
| Nitrosylation on C | UNIMOD:275 | 10 |
| Water Loss on E | UNIMOD:27 | 10 |
| Cu[I] on D | UNIMOD:531 | 9 |
| Hydroxyproline on P | UNIMOD:35 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 6 |
| Dimethylated arginine on R | UNIMOD:36 | 5 |
| N6-glutaryllysine on K | — | 5 |
| Phosphorylation on Y | UNIMOD:21 | 5 |
| Zinc on D | UNIMOD:954 | 5 |
| Allysine on K | UNIMOD:352 | 4 |
| Citrulline on R | UNIMOD:7 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| N6-butyryllysine on K | UNIMOD:1289 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Cu[I] on E | UNIMOD:531 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 3 |
| N6-methacryllysine on K | — | 3 |
| Sulfonation on Y | UNIMOD:40 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-crotonyllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 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 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
791a8396dbfb012c, written 2026-10-30T12:39:46+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