Generated summary
PXD028865 is a DDA label-free dataset (Mus musculus) with 32 runs, 32 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,028,186 PSMs, 37,114 peptidoforms and 3,179 protein groups, and the repository holds 30,774 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 1.02819e+06 where the producer reported 1.02828e+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 1.02819e+06 where the producer reported 1.02828e+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
14.75% of protein intensity in the worst file, 9.70% median across 32 files (DEF-QC-9 v3.5)
14.75% of protein intensity in the worst file, 9.70% median across 32 files (DEF-QC-9 v3.5)
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 160103 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6237 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 160103 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6237 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: 57719 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: 57719 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. PXD028865:F7CNS2;L7MU46 written 2 times; quant_values: 64 identifier(s), 64 row(s) dropped, e.g. PXD028865:E2021200299a:label_free:protein_group:PXD028865:F7CNS2;L7MU46: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. PXD028865:F7CNS2;L7MU46 written 2 times; quant_values: 64 identifier(s), 64 row(s) dropped, e.g. PXD028865:E2021200299a:label_free:protein_group:PXD028865:F7CNS2;L7MU46:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
160 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
160 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 | 1,028,186 |
| Peptidoforms at 1% FDR | 37,114 |
| Protein groups at 1% FDR | 3,179 |
| PTM sites | 30,774 |
| Quantitative values | 759,452 |
| PSMs, all (including decoys and sub-threshold) | 1,584,197 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 36.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 11.5% |
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
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 32 / 32
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 16929cfb36e7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 10,327 |
| Oxidation on M | UNIMOD:35 | 1,685 |
| Fe[III] on E | UNIMOD:1870 | 1,551 |
| Fe[II] on E | UNIMOD:952 | 1,102 |
| Deamidation on N | UNIMOD:7 | 1,043 |
| Deamidation on Q | UNIMOD:7 | 1,036 |
| Carbamyl on X | UNIMOD:5 | 984 |
| Hydroxylation on P | UNIMOD:35 | 961 |
| Fe[III] on D | UNIMOD:1870 | 807 |
| Ammonia loss on N | UNIMOD:385 | 632 |
| Carbamyl on K | UNIMOD:5 | 629 |
| Fe[II] on D | UNIMOD:952 | 583 |
| Citrullination on R | UNIMOD:7 | 579 |
| Hydroxylation on K | UNIMOD:35 | 560 |
| Phosphorylation on T | UNIMOD:21 | 454 |
| Hydroxylation on N | UNIMOD:35 | 439 |
| Sodium on E | UNIMOD:30 | 384 |
| Methylation on K | UNIMOD:34 | 353 |
| Phosphorylation on S | UNIMOD:21 | 348 |
| Trimethylation on K | UNIMOD:37 | 347 |
| Acetylation on K | UNIMOD:1 | 293 |
| Ammonia loss on C | UNIMOD:385 | 271 |
| Cu[I] on E | UNIMOD:531 | 271 |
| Zinc on E | UNIMOD:954 | 268 |
| HexNAc on T | UNIMOD:43 | 256 |
| Phosphoserine on S | UNIMOD:21 | 250 |
| Dimethylation on K | UNIMOD:36 | 213 |
| Carbamyl on C | UNIMOD:5 | 175 |
| Acetylation on X | UNIMOD:1 | 165 |
| Water Loss on E | UNIMOD:27 | 163 |
| Phosphorylation on Y | UNIMOD:21 | 156 |
| HexNAc on S | UNIMOD:43 | 149 |
| Sulfonation on Y | UNIMOD:40 | 143 |
| Carboxylation on E | UNIMOD:299 | 135 |
| N-acetylalanine on A | UNIMOD:1 | 130 |
| Magnesium on E | UNIMOD:956 | 122 |
| Carboxylation on K | UNIMOD:299 | 121 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 117 |
| Formylation on K | UNIMOD:122 | 92 |
| Methylation on R | UNIMOD:34 | 86 |
| Glutarylation on K | UNIMOD:1848 | 83 |
| Sodium on D | UNIMOD:30 | 83 |
| N-acetylmethionine on M | UNIMOD:1 | 69 |
| Dimethylation on R | UNIMOD:36 | 67 |
| Carbamyl on R | UNIMOD:5 | 60 |
| Calcium on E | UNIMOD:951 | 58 |
| Potassium on E | UNIMOD:530 | 58 |
| N-acetylserine on S | UNIMOD:1 | 56 |
| Magnesium on D | UNIMOD:956 | 55 |
| N6-acetyllysine on K | UNIMOD:1 | 54 |
| Nitrosylation on C | UNIMOD:275 | 50 |
| Succinylation on K | UNIMOD:64 | 50 |
| Phosphothreonine on T | UNIMOD:21 | 48 |
| Calcium on D | UNIMOD:951 | 41 |
| Cu[I] on D | UNIMOD:531 | 39 |
| Zinc on D | UNIMOD:954 | 38 |
| Carbamyl on M | UNIMOD:5 | 34 |
| Nitrosylation on Y | UNIMOD:354 | 31 |
| Potassium on D | UNIMOD:530 | 30 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 28 |
| Omega-N-methylarginine on R | UNIMOD:34 | 27 |
| Hydroxybutyrylation on K | — | 23 |
| Butyrylation on K | UNIMOD:1289 | 21 |
| Carboxylation on D | UNIMOD:299 | 18 |
| Crotonylation on K | UNIMOD:1363 | 17 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| 4-hydroxyproline on P | UNIMOD:35 | 10 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 10 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| Phosphotyrosine on Y | UNIMOD:21 | 8 |
| Deamidated asparagine on N | UNIMOD:7 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| Citrulline on R | UNIMOD:7 | 5 |
| N6-glutaryllysine on K | — | 5 |
| HexNAc on Nxs | UNIMOD:43 | 4 |
| N6-succinyllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| Pyridoxal phosphate on K | UNIMOD:46 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine methyl ester on C | UNIMOD:34 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-methacryllysine on K | — | 1 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Sulfocysteine on C | UNIMOD:40 | 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
901bafe9fa5d4c55, written 2026-10-29T12:44:54+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