Generated summary
PXD054290 is a DDA label-free dataset (Mus musculus) 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 1,403,775 PSMs, 30,076 peptidoforms and 4,144 protein groups, and the repository holds 26,926 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 1.40378e+06 where the producer reported 1.40381e+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 1.40378e+06 where the producer reported 1.40381e+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.
high_contamination warning
5.54% of protein intensity in the worst file, 3.55% median across 20 files (DEF-QC-9 v3.5)
5.54% of protein intensity in the worst file, 3.55% median across 20 files (DEF-QC-9 v3.5)
occupancy_not_stored warning
Of 71454 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 15490 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 71454 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 15490 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_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: Primary cell. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: Primary cell. Match on it as text; it has not been mapped to a term.
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: 5367 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: 5367 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: 5 identifier(s), 5 row(s) dropped, e.g. PXD054290:A0A6B9UF22;A0A9L6KE92 written 2 times; quant_values: 100 identifier(s), 100 row(s) dropped, e.g. PXD054290:Service_20220202_Mireille_Ouimet_01:label_free:protein_group:PXD054290:A0A6B9UF22;A0A9L6KE92: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: 5 identifier(s), 5 row(s) dropped, e.g. PXD054290:A0A6B9UF22;A0A9L6KE92 written 2 times; quant_values: 100 identifier(s), 100 row(s) dropped, e.g. PXD054290:Service_20220202_Mireille_Ouimet_01:label_free:protein_group:PXD054290:A0A6B9UF22;A0A9L6KE92:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
124 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
124 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 | 1,403,775 |
| Peptidoforms at 1% FDR | 30,076 |
| Protein groups at 1% FDR | 4,144 |
| PTM sites | 26,926 |
| Quantitative values | 770,648 |
| PSMs, all (including decoys and sub-threshold) | 3,502,632 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 45.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.8% |
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
- Thermo
- Runs / samples
- 20 / 20
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 852cea5e1cd7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 8,998 |
| Oxidation on M | UNIMOD:35 | 6,458 |
| Deamidation on N | UNIMOD:7 | 1,609 |
| Deamidation on Q | UNIMOD:7 | 1,487 |
| Carbamyl on X | UNIMOD:5 | 1,158 |
| Hydroxylation on P | UNIMOD:35 | 867 |
| Hydroxylation on N | UNIMOD:35 | 486 |
| Citrullination on R | UNIMOD:7 | 392 |
| N-acetylalanine on A | UNIMOD:1 | 333 |
| Hydroxylation on K | UNIMOD:35 | 324 |
| Sodium on E | UNIMOD:30 | 231 |
| Sodium on D | UNIMOD:30 | 229 |
| Ammonia loss on N | UNIMOD:385 | 224 |
| Carbamyl on K | UNIMOD:5 | 223 |
| Acetylation on X | UNIMOD:1 | 198 |
| Magnesium on D | UNIMOD:956 | 198 |
| Magnesium on E | UNIMOD:956 | 169 |
| Methylation on K | UNIMOD:34 | 161 |
| Water Loss on E | UNIMOD:27 | 134 |
| N-acetylmethionine on M | UNIMOD:1 | 127 |
| Phosphoserine on S | UNIMOD:21 | 125 |
| N-acetylserine on S | UNIMOD:1 | 120 |
| Calcium on D | UNIMOD:951 | 94 |
| N6-acetyllysine on K | UNIMOD:1 | 89 |
| Ammonia loss on C | UNIMOD:385 | 82 |
| Phosphorylation on S | UNIMOD:21 | 75 |
| Acetylation on K | UNIMOD:1 | 73 |
| Carbamyl on M | UNIMOD:5 | 68 |
| Potassium on D | UNIMOD:530 | 64 |
| Carbamyl on R | UNIMOD:5 | 60 |
| Phosphorylation on T | UNIMOD:21 | 59 |
| Calcium on E | UNIMOD:951 | 57 |
| Dimethylation on K | UNIMOD:36 | 44 |
| HexNAc on S | UNIMOD:43 | 42 |
| Methylation on R | UNIMOD:34 | 42 |
| Fe[III] on D | UNIMOD:1870 | 38 |
| Fe[III] on E | UNIMOD:1870 | 37 |
| Potassium on E | UNIMOD:530 | 37 |
| Carboxylation on D | UNIMOD:299 | 33 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 30 |
| HexNAc on T | UNIMOD:43 | 29 |
| N-acetylthreonine on T | UNIMOD:1 | 29 |
| Malonylation on K | UNIMOD:747 | 26 |
| Dimethylation on R | UNIMOD:36 | 25 |
| Fe[II] on D | UNIMOD:952 | 23 |
| Formylation on K | UNIMOD:122 | 21 |
| Trimethylation on K | UNIMOD:37 | 21 |
| N6-methyllysine on K | UNIMOD:34 | 20 |
| Carbamyl on C | UNIMOD:5 | 19 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 19 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 19 |
| Nitrosylation on Y | UNIMOD:354 | 19 |
| Phosphothreonine on T | UNIMOD:21 | 19 |
| Crotonylation on K | UNIMOD:1363 | 18 |
| Omega-N-methylarginine on R | UNIMOD:34 | 17 |
| Carboxylation on E | UNIMOD:299 | 15 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| Hydroxybutyrylation on K | — | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 14 |
| 4-hydroxyproline on P | UNIMOD:35 | 13 |
| Butyrylation on K | UNIMOD:1289 | 13 |
| Phosphorylation on Y | UNIMOD:21 | 13 |
| Glutarylation on K | UNIMOD:1848 | 12 |
| Carboxylation on K | UNIMOD:299 | 11 |
| Cu[I] on D | UNIMOD:531 | 11 |
| Fe[II] on E | UNIMOD:952 | 11 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 10 |
| N6-succinyllysine on K | — | 9 |
| Phosphotyrosine on Y | UNIMOD:21 | 9 |
| Succinylation on K | UNIMOD:64 | 9 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| N6-crotonyllysine on K | — | 6 |
| Cu[I] on E | UNIMOD:531 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N5-methylglutamine on Q | UNIMOD:34 | 5 |
| Nitrosylation on C | UNIMOD:275 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 4 |
| N6-methacryllysine on K | — | 4 |
| Sulfonation on Y | UNIMOD:40 | 4 |
| N6-malonyllysine on K | — | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N-acetylproline on P | UNIMOD:1 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-lipoyllysine on K | UNIMOD:42 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| Zinc on D | UNIMOD:954 | 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
a05fbea863dba7de, written 2026-10-29T11:27:46+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