Generated summary
PXD024478 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 469,358 PSMs, 73,419 peptidoforms and 7,044 protein groups, and the repository holds 32,060 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 2 for information
count_mismatch warning
The bundle holds 469358 where the producer reported 469375 (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 469358 where the producer reported 469375 (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.
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 39452 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3920 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 39452 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3920 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).
spectral_library warning
human's current library moved from version 83 to 84 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD024478\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-22-05-06.msp and has NOT been registered, so nothing was lost; merge it deliberately.
human's current library moved from version 83 to 84 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD024478\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-22-05-06.msp and has NOT been registered, so nothing was lost; merge it deliberately.
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: 942 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: 942 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.
collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD024478:M0QZD8;Q6ZTK2 written 2 times; quant_values: 20 identifier(s), 20 row(s) dropped, e.g. PXD024478:BBM_321_P153_02_FRH_001:label_free:protein_group:PXD024478:M0QZD8;Q6ZTK2:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD024478:M0QZD8;Q6ZTK2 written 2 times; quant_values: 20 identifier(s), 20 row(s) dropped, e.g. PXD024478:BBM_321_P153_02_FRH_001:label_free:protein_group:PXD024478:M0QZD8;Q6ZTK2:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
27 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
27 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 | 469,358 |
| Peptidoforms at 1% FDR | 73,419 |
| Protein groups at 1% FDR | 7,044 |
| PTM sites | 32,060 |
| Quantitative values | 498,411 |
| PSMs, all (including decoys and sub-threshold) | 1,379,624 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 41.6% |
| 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
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 16,166 |
| Oxidation on M | UNIMOD:35 | 4,271 |
| Deamidation on N | UNIMOD:7 | 3,074 |
| Deamidation on Q | UNIMOD:7 | 2,752 |
| Hydroxylation on P | UNIMOD:35 | 615 |
| Phosphoserine on S | UNIMOD:21 | 437 |
| Ammonia loss on N | UNIMOD:385 | 364 |
| Citrullination on R | UNIMOD:7 | 315 |
| Hydroxylation on N | UNIMOD:35 | 291 |
| Fe[III] on E | UNIMOD:1870 | 247 |
| N-acetylalanine on A | UNIMOD:1 | 225 |
| Fe[III] on D | UNIMOD:1870 | 204 |
| Water Loss on E | UNIMOD:27 | 181 |
| Methylation on K | UNIMOD:34 | 151 |
| Carbamyl on X | UNIMOD:5 | 144 |
| Fe[II] on E | UNIMOD:952 | 144 |
| Hydroxylation on K | UNIMOD:35 | 129 |
| N-acetylmethionine on M | UNIMOD:1 | 125 |
| Phosphorylation on S | UNIMOD:21 | 111 |
| Acetylation on X | UNIMOD:1 | 105 |
| Fe[II] on D | UNIMOD:952 | 100 |
| N-acetylserine on S | UNIMOD:1 | 89 |
| Phosphorylation on T | UNIMOD:21 | 86 |
| Calcium on E | UNIMOD:951 | 82 |
| Ammonia loss on C | UNIMOD:385 | 81 |
| Magnesium on D | UNIMOD:956 | 72 |
| Acetylation on K | UNIMOD:1 | 66 |
| Methylation on R | UNIMOD:34 | 66 |
| Magnesium on E | UNIMOD:956 | 63 |
| Trimethylation on K | UNIMOD:37 | 55 |
| Dimethylation on R | UNIMOD:36 | 53 |
| N6-acetyllysine on K | UNIMOD:1 | 52 |
| Phosphothreonine on T | UNIMOD:21 | 49 |
| Sodium on D | UNIMOD:30 | 49 |
| Calcium on D | UNIMOD:951 | 46 |
| Sodium on E | UNIMOD:30 | 43 |
| Omega-N-methylarginine on R | UNIMOD:34 | 42 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 40 |
| Formylation on K | UNIMOD:122 | 38 |
| HexNAc on S | UNIMOD:43 | 37 |
| Dimethylation on K | UNIMOD:36 | 35 |
| HexNAc on T | UNIMOD:43 | 34 |
| Carbamyl on M | UNIMOD:5 | 28 |
| Potassium on E | UNIMOD:530 | 24 |
| Carboxylation on E | UNIMOD:299 | 22 |
| N-acetylthreonine on T | UNIMOD:1 | 21 |
| Potassium on D | UNIMOD:530 | 20 |
| Carbamyl on C | UNIMOD:5 | 19 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| N6-methyllysine on K | UNIMOD:34 | 18 |
| Phosphorylation on Y | UNIMOD:21 | 18 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 17 |
| Crotonylation on K | UNIMOD:1363 | 16 |
| Succinylation on K | UNIMOD:64 | 16 |
| Cu[I] on E | UNIMOD:531 | 15 |
| Sulfonation on Y | UNIMOD:40 | 15 |
| Malonylation on K | UNIMOD:747 | 14 |
| Nitrosylation on Y | UNIMOD:354 | 14 |
| Cu[I] on D | UNIMOD:531 | 13 |
| Pyridoxal phosphate on K | UNIMOD:46 | 13 |
| Carbamyl on K | UNIMOD:5 | 12 |
| Carboxylation on D | UNIMOD:299 | 12 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 11 |
| Nitrosylation on C | UNIMOD:275 | 11 |
| Butyrylation on K | UNIMOD:1289 | 10 |
| Carboxylation on K | UNIMOD:299 | 10 |
| Carbamyl on R | UNIMOD:5 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| N5-methylglutamine on Q | UNIMOD:34 | 8 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| Glutarylation on K | UNIMOD:1848 | 7 |
| Hydroxybutyrylation on K | — | 7 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| HexNAc on Nxt | UNIMOD:43 | 4 |
| N-myristoyl glycine on G | UNIMOD:45 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-succinyllysine on K | — | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-crotonyllysine on K | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
c1108f19cba7fd3f, written 2026-10-29T09:37:08+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