Generated summary
PXD006815 is a DDA label-free dataset (Mus musculus) with 36 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,142,250 PSMs, 101,104 peptidoforms and 7,685 protein groups, and the repository holds 40,002 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 1.14225e+06 where the producer reported 1.14255e+06 (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 1.14225e+06 where the producer reported 1.14255e+06 (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.
cysteine_poor warning
4.68% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
4.68% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
occupancy_not_stored warning
Of 208355 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11789 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 208355 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11789 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).
sdrf_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 3379 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: 3379 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: 3 identifier(s), 5 row(s) dropped, e.g. PXD006815:A0A0J9YUM1;A0A571BEB1;A0AAG1GAD3;A0AAG1GHQ8;A0AAG1GLY0;K9J7D1 written 4 times; quant_values: 36 identifier(s), 60 row(s) dropped, e.g. PXD006815:design:A_1:protein_group:PXD006815:A0A0J9YUM1;A0A571BEB1;A0AAG1GAD3;A0AAG1GHQ8;A0AAG1GLY0;K9J7D1:QuantProject:DEF-PROT-SPC written 4 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: 3 identifier(s), 5 row(s) dropped, e.g. PXD006815:A0A0J9YUM1;A0A571BEB1;A0AAG1GAD3;A0AAG1GHQ8;A0AAG1GLY0;K9J7D1 written 4 times; quant_values: 36 identifier(s), 60 row(s) dropped, e.g. PXD006815:design:A_1:protein_group:PXD006815:A0A0J9YUM1;A0A571BEB1;A0AAG1GAD3;A0AAG1GHQ8;A0AAG1GLY0;K9J7D1:QuantProject:DEF-PROT-SPC written 4 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
142 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
142 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 | 1,142,250 |
| Peptidoforms at 1% FDR | 101,104 |
| Protein groups at 1% FDR | 7,685 |
| PTM sites | 40,002 |
| Quantitative values | 977,622 |
| PSMs, all (including decoys and sub-threshold) | 2,749,944 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 43.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.0% |
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
- 36 / 12
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 12,327 |
| Deamidation on N | UNIMOD:7 | 7,521 |
| Deamidation on Q | UNIMOD:7 | 4,957 |
| Citrullination on R | UNIMOD:7 | 2,719 |
| Hydroxylation on P | UNIMOD:35 | 1,626 |
| Ammonia loss on N | UNIMOD:385 | 1,068 |
| Hydroxylation on N | UNIMOD:35 | 766 |
| Carbamyl on X | UNIMOD:5 | 550 |
| Formylation on K | UNIMOD:122 | 464 |
| Water Loss on E | UNIMOD:27 | 461 |
| Hydroxylation on K | UNIMOD:35 | 442 |
| Acetylation on X | UNIMOD:1 | 398 |
| Phosphorylation on S | UNIMOD:21 | 375 |
| N-acetylalanine on A | UNIMOD:1 | 358 |
| Phosphoserine on S | UNIMOD:21 | 349 |
| Methylation on R | UNIMOD:34 | 332 |
| Phosphorylation on T | UNIMOD:21 | 300 |
| Methylation on K | UNIMOD:34 | 287 |
| Acetylation on K | UNIMOD:1 | 191 |
| N6-acetyllysine on K | UNIMOD:1 | 167 |
| HexNAc on S | UNIMOD:43 | 166 |
| Dimethylation on R | UNIMOD:36 | 163 |
| Sodium on E | UNIMOD:30 | 146 |
| N-acetylmethionine on M | UNIMOD:1 | 143 |
| Sulfonation on Y | UNIMOD:40 | 142 |
| Carbamyl on K | UNIMOD:5 | 132 |
| HexNAc on T | UNIMOD:43 | 129 |
| Carbamyl on M | UNIMOD:5 | 126 |
| Crotonylation on K | UNIMOD:1363 | 122 |
| N-acetylserine on S | UNIMOD:1 | 117 |
| Phosphothreonine on T | UNIMOD:21 | 110 |
| Magnesium on E | UNIMOD:956 | 106 |
| Dimethylation on K | UNIMOD:36 | 104 |
| Sodium on D | UNIMOD:30 | 96 |
| Trimethylation on K | UNIMOD:37 | 92 |
| Omega-N-methylarginine on R | UNIMOD:34 | 88 |
| Carboxylation on E | UNIMOD:299 | 82 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 79 |
| Butyrylation on K | UNIMOD:1289 | 79 |
| Fe[III] on E | UNIMOD:1870 | 74 |
| Carbamyl on R | UNIMOD:5 | 69 |
| Carboxylation on D | UNIMOD:299 | 66 |
| Magnesium on D | UNIMOD:956 | 62 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 60 |
| Nitrosylation on C | UNIMOD:275 | 57 |
| Fe[III] on D | UNIMOD:1870 | 56 |
| Fe[II] on E | UNIMOD:952 | 55 |
| Malonylation on K | UNIMOD:747 | 51 |
| 4-hydroxyproline on P | UNIMOD:35 | 50 |
| Nitrosylation on Y | UNIMOD:354 | 49 |
| N6-methyllysine on K | UNIMOD:34 | 43 |
| N6-succinyllysine on K | — | 37 |
| Carboxylation on K | UNIMOD:299 | 34 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 33 |
| Carbamyl on C | UNIMOD:5 | 30 |
| N-acetylthreonine on T | UNIMOD:1 | 30 |
| Fe[II] on D | UNIMOD:952 | 28 |
| Glutarylation on K | UNIMOD:1848 | 28 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 28 |
| Succinylation on K | UNIMOD:64 | 28 |
| Hydroxybutyrylation on K | — | 25 |
| Phosphorylation on Y | UNIMOD:21 | 18 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 16 |
| N-myristoyl glycine on G | UNIMOD:45 | 14 |
| Ammonia loss on C | UNIMOD:385 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| N6-methacryllysine on K | — | 12 |
| Pyridoxal phosphate on K | UNIMOD:46 | 11 |
| Citrulline on R | UNIMOD:7 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 10 |
| Phosphotyrosine on Y | UNIMOD:21 | 9 |
| Calcium on E | UNIMOD:951 | 8 |
| N6-butyryllysine on K | UNIMOD:1289 | 8 |
| Cu[I] on D | UNIMOD:531 | 7 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| N6-glutaryllysine on K | — | 7 |
| Potassium on D | UNIMOD:530 | 7 |
| N6-malonyllysine on K | — | 6 |
| Potassium on E | UNIMOD:530 | 6 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-benzoyllysine on K | UNIMOD:136 | 5 |
| N6-crotonyllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Cu[I] on E | UNIMOD:531 | 4 |
| HexNAc on Nxt | UNIMOD:43 | 4 |
| N6-lipoyllysine on K | UNIMOD:42 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Calcium on D | UNIMOD:951 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-(pyridoxal phosphate)lysine on K | UNIMOD:46 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| Phosphohistidine on H | UNIMOD:21 | 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
712d0d04e45dc132, written 2026-10-29T11:35:26+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