Generated summary
PXD024685 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 835,173 PSMs, 44,479 peptidoforms and 4,821 protein groups, and the repository holds 21,618 PTM sites for it. 4 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, 4 warnings and 2 for information
count_mismatch warning
The bundle holds 835173 where the producer reported 835215 (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 835173 where the producer reported 835215 (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 100428 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 20 duplicate entry for one site and run (identical values; same protein group); 26289 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 100428 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 20 duplicate entry for one site and run (identical values; same protein group); 26289 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: 2078 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: 2078 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), 4 row(s) dropped, e.g. PXD024685:A0A9L6KDF6;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6 written 5 times; quant_values: 30 identifier(s), 120 row(s) dropped, e.g. PXD024685:0164-141014MaJoS01TQ_141022131630:label_free:protein_group:PXD024685:A0A9L6KDF6;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 5 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), 4 row(s) dropped, e.g. PXD024685:A0A9L6KDF6;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6 written 5 times; quant_values: 30 identifier(s), 120 row(s) dropped, e.g. PXD024685:0164-141014MaJoS01TQ_141022131630:label_free:protein_group:PXD024685:A0A9L6KDF6;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 5 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
49 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
49 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 | 835,173 |
| Peptidoforms at 1% FDR | 44,479 |
| Protein groups at 1% FDR | 4,821 |
| PTM sites | 21,618 |
| Quantitative values | 1,229,426 |
| PSMs, all (including decoys and sub-threshold) | 1,744,083 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 48.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.0% |
How it was measured
- Organism searched
- Mus musculus (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
- 30 / 30
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- a086cd029e63
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 9,000 |
| Oxidation on M | UNIMOD:35 | 3,654 |
| Fe[III] on E | UNIMOD:1870 | 918 |
| Fe[III] on D | UNIMOD:1870 | 775 |
| Deamidation on N | UNIMOD:7 | 734 |
| Hydroxylation on P | UNIMOD:35 | 532 |
| Deamidation on Q | UNIMOD:7 | 449 |
| Ammonia loss on N | UNIMOD:385 | 395 |
| Ammonia loss on C | UNIMOD:385 | 393 |
| N-acetylalanine on A | UNIMOD:1 | 368 |
| Acetylation on X | UNIMOD:1 | 324 |
| Hydroxylation on N | UNIMOD:35 | 313 |
| Calcium on E | UNIMOD:951 | 292 |
| Calcium on D | UNIMOD:951 | 253 |
| Hydroxylation on K | UNIMOD:35 | 251 |
| Sodium on E | UNIMOD:30 | 225 |
| Sodium on D | UNIMOD:30 | 201 |
| N-acetylmethionine on M | UNIMOD:1 | 182 |
| Nitrosylation on Y | UNIMOD:354 | 178 |
| N-acetylserine on S | UNIMOD:1 | 157 |
| Phosphoserine on S | UNIMOD:21 | 138 |
| Carbamyl on X | UNIMOD:5 | 134 |
| Fe[II] on E | UNIMOD:952 | 114 |
| Citrullination on R | UNIMOD:7 | 111 |
| Fe[II] on D | UNIMOD:952 | 109 |
| Magnesium on E | UNIMOD:956 | 108 |
| N6-acetyllysine on K | UNIMOD:1 | 103 |
| Magnesium on D | UNIMOD:956 | 101 |
| Water Loss on E | UNIMOD:27 | 99 |
| Potassium on D | UNIMOD:530 | 62 |
| Methylation on K | UNIMOD:34 | 61 |
| Phosphorylation on S | UNIMOD:21 | 54 |
| Potassium on E | UNIMOD:530 | 52 |
| Acetylation on K | UNIMOD:1 | 39 |
| Formylation on K | UNIMOD:122 | 36 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 32 |
| N-acetylthreonine on T | UNIMOD:1 | 31 |
| Phosphorylation on T | UNIMOD:21 | 29 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 26 |
| Dimethylation on K | UNIMOD:36 | 25 |
| Carbamyl on K | UNIMOD:5 | 21 |
| Phosphothreonine on T | UNIMOD:21 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 20 |
| Trimethylation on K | UNIMOD:37 | 20 |
| Methylation on R | UNIMOD:34 | 19 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| N-myristoyl glycine on G | UNIMOD:45 | 17 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 16 |
| N6-succinyllysine on K | — | 15 |
| Carboxylation on E | UNIMOD:299 | 13 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| Carboxylation on D | UNIMOD:299 | 12 |
| Crotonylation on K | UNIMOD:1363 | 12 |
| Glutarylation on K | UNIMOD:1848 | 12 |
| Omega-N-methylarginine on R | UNIMOD:34 | 12 |
| Carboxylation on K | UNIMOD:299 | 11 |
| Hydroxybutyrylation on K | — | 11 |
| N6-methyllysine on K | UNIMOD:34 | 11 |
| Dimethylation on R | UNIMOD:36 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 10 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 9 |
| Succinylation on K | UNIMOD:64 | 8 |
| N-acetylvaline on V | UNIMOD:1 | 7 |
| HexNAc on S | UNIMOD:43 | 6 |
| HexNAc on T | UNIMOD:43 | 6 |
| N6-crotonyllysine on K | — | 6 |
| Phosphorylation on Y | UNIMOD:21 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 5 |
| N6-glutaryllysine on K | — | 5 |
| Pyridoxal phosphate on K | UNIMOD:46 | 5 |
| Carbamyl on M | UNIMOD:5 | 4 |
| Carbamyl on R | UNIMOD:5 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Glu to PyroGlu on Q | UNIMOD:28 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Zinc on E | UNIMOD:954 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Cu[I] on D | UNIMOD:531 | 2 |
| Cu[I] on E | UNIMOD:531 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Hypusine on K | UNIMOD:379 | 2 |
| N-acetylproline on P | UNIMOD:1 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-malonyllysine on K | — | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Sulfonation on Y | UNIMOD:40 | 2 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 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-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 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
3a0d44815d25b5da, written 2026-10-29T12:32:38+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