Generated summary
PXD025280 is a DDA label-free dataset (Homo sapiens) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 214,292 PSMs, 19,885 peptidoforms and 3,273 protein groups, and the repository holds 8,453 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 214292 where the producer reported 214295 (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 214292 where the producer reported 214295 (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
15.71 avg cores of 32 allowed (S5)
15.71 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 30161 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4192 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 30161 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4192 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).
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: 447 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: 447 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD025280:P49916;P49916-3 written 2 times; quant_values: 32 identifier(s), 32 row(s) dropped, e.g. PXD025280:20170706_JS_JL_01:label_free:protein_group:PXD025280:P49916;P49916-3: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: 2 identifier(s), 2 row(s) dropped, e.g. PXD025280:P49916;P49916-3 written 2 times; quant_values: 32 identifier(s), 32 row(s) dropped, e.g. PXD025280:20170706_JS_JL_01:label_free:protein_group:PXD025280:P49916;P49916-3:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
14 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
14 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 | 214,292 |
| Peptidoforms at 1% FDR | 19,885 |
| Protein groups at 1% FDR | 3,273 |
| PTM sites | 8,453 |
| Quantitative values | 371,909 |
| PSMs, all (including decoys and sub-threshold) | 428,203 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 31.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.3% |
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
- 16 / 16
- 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 | 3,847 |
| Deamidation on Q | UNIMOD:7 | 499 |
| Sodium on E | UNIMOD:30 | 458 |
| Deamidation on N | UNIMOD:7 | 382 |
| Sodium on D | UNIMOD:30 | 355 |
| Oxidation on M | UNIMOD:35 | 264 |
| Calcium on E | UNIMOD:951 | 253 |
| Calcium on D | UNIMOD:951 | 208 |
| N-acetylalanine on A | UNIMOD:1 | 181 |
| Ammonia loss on N | UNIMOD:385 | 143 |
| Carbamyl on M | UNIMOD:5 | 143 |
| Hydroxylation on P | UNIMOD:35 | 111 |
| Phosphoserine on S | UNIMOD:21 | 96 |
| Carbamyl on X | UNIMOD:5 | 91 |
| Magnesium on E | UNIMOD:956 | 87 |
| Methylation on K | UNIMOD:34 | 85 |
| N-acetylserine on S | UNIMOD:1 | 60 |
| Magnesium on D | UNIMOD:956 | 58 |
| Ammonia loss on C | UNIMOD:385 | 52 |
| Acetylation on K | UNIMOD:1 | 49 |
| Methylation on R | UNIMOD:34 | 42 |
| Phosphorylation on S | UNIMOD:21 | 40 |
| Potassium on E | UNIMOD:530 | 31 |
| Fe[II] on E | UNIMOD:952 | 29 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 29 |
| Acetylation on X | UNIMOD:1 | 27 |
| Citrullination on R | UNIMOD:7 | 27 |
| Phosphorylation on T | UNIMOD:21 | 25 |
| Trimethylation on K | UNIMOD:37 | 23 |
| N6-acetyllysine on K | UNIMOD:1 | 22 |
| Water Loss on E | UNIMOD:27 | 20 |
| 4-hydroxyproline on P | UNIMOD:35 | 19 |
| Carboxylation on D | UNIMOD:299 | 19 |
| Potassium on D | UNIMOD:530 | 17 |
| Hydroxylation on K | UNIMOD:35 | 16 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 16 |
| N-acetylmethionine on M | UNIMOD:1 | 15 |
| Fe[II] on D | UNIMOD:952 | 14 |
| Glutarylation on K | UNIMOD:1848 | 13 |
| Carboxylation on E | UNIMOD:299 | 12 |
| Dimethylation on K | UNIMOD:36 | 12 |
| HexNAc on S | UNIMOD:43 | 12 |
| Hydroxylation on N | UNIMOD:35 | 12 |
| N-acetylthreonine on T | UNIMOD:1 | 12 |
| Dimethylation on R | UNIMOD:36 | 11 |
| N6-methyllysine on K | UNIMOD:34 | 11 |
| Omega-N-methylarginine on R | UNIMOD:34 | 11 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 10 |
| Carbamyl on K | UNIMOD:5 | 10 |
| HexNAc on T | UNIMOD:43 | 10 |
| Butyrylation on K | UNIMOD:1289 | 9 |
| Fe[III] on E | UNIMOD:1870 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 7 |
| Phosphorylation on Y | UNIMOD:21 | 7 |
| Phosphothreonine on T | UNIMOD:21 | 7 |
| Carbamyl on C | UNIMOD:5 | 6 |
| Carbamyl on R | UNIMOD:5 | 6 |
| Sulfonation on Y | UNIMOD:40 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| Fe[III] on D | UNIMOD:1870 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| Malonylation on K | UNIMOD:747 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carboxylation on K | UNIMOD:299 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Formylation on K | UNIMOD:122 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-glutaryllysine on K | — | 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
d35be1b4df2cf457, written 2026-10-29T09:11:37+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