Generated summary
PXD032240 is a DDA label-free dataset (Mus musculus) with 24 runs, 24 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 375,188 PSMs, 34,716 peptidoforms and 3,131 protein groups, and the repository holds 25,201 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 375188 where the producer reported 375252 (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 375188 where the producer reported 375252 (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
23.28% of protein intensity in the worst file, 6.64% median across 24 files (DEF-QC-9 v3.5)
23.28% of protein intensity in the worst file, 6.64% median across 24 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 85112 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4703 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 85112 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4703 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: 7619 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: 7619 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), 10 row(s) dropped, e.g. PXD032240:A0A6B9UF22;A0A9L6KDF6;A0A9L6KDQ4;A0A9L6KDR4;A0A9L6KDR9;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KE99;A0A9L6KEA6;A0A9L6KEB1 written 11 times; quant_values: 24 identifier(s), 240 row(s) dropped, e.g. PXD032240:q104704a:label_free:protein_group:PXD032240:A0A6B9UF22;A0A9L6KDF6;A0A9L6KDQ4;A0A9L6KDR4;A0A9L6KDR9;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KE99;A0A9L6KEA6;A0A9L6KEB1:QuantProject:DEF-PROT-SPC written 11 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), 10 row(s) dropped, e.g. PXD032240:A0A6B9UF22;A0A9L6KDF6;A0A9L6KDQ4;A0A9L6KDR4;A0A9L6KDR9;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KE99;A0A9L6KEA6;A0A9L6KEB1 written 11 times; quant_values: 24 identifier(s), 240 row(s) dropped, e.g. PXD032240:q104704a:label_free:protein_group:PXD032240:A0A6B9UF22;A0A9L6KDF6;A0A9L6KDQ4;A0A9L6KDR4;A0A9L6KDR9;A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE92;A0A9L6KE99;A0A9L6KEA6;A0A9L6KEB1:QuantProject:DEF-PROT-SPC written 11 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
81 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
81 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 | 375,188 |
| Peptidoforms at 1% FDR | 34,716 |
| Protein groups at 1% FDR | 3,131 |
| PTM sites | 25,201 |
| Quantitative values | 513,559 |
| PSMs, all (including decoys and sub-threshold) | 672,142 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 52.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 5.2% |
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
- 24 / 24
- Sample metadata
- absent
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 7,980 |
| Deamidation on Q | UNIMOD:7 | 2,651 |
| Oxidation on M | UNIMOD:35 | 2,446 |
| Deamidation on N | UNIMOD:7 | 2,084 |
| Hydroxylation on P | UNIMOD:35 | 1,476 |
| Citrullination on R | UNIMOD:7 | 763 |
| Hydroxylation on N | UNIMOD:35 | 571 |
| Hydroxylation on K | UNIMOD:35 | 566 |
| Fe[III] on E | UNIMOD:1870 | 473 |
| Ammonia loss on N | UNIMOD:385 | 336 |
| Fe[III] on D | UNIMOD:1870 | 240 |
| Nitrosylation on Y | UNIMOD:354 | 237 |
| Phosphorylation on Y | UNIMOD:21 | 227 |
| Carbamyl on X | UNIMOD:5 | 217 |
| Nitrosylation on C | UNIMOD:275 | 217 |
| Phosphoserine on S | UNIMOD:21 | 199 |
| Ammonia loss on C | UNIMOD:385 | 176 |
| Phosphorylation on S | UNIMOD:21 | 175 |
| Fe[II] on E | UNIMOD:952 | 174 |
| Methylation on K | UNIMOD:34 | 170 |
| Magnesium on E | UNIMOD:956 | 145 |
| Fe[II] on D | UNIMOD:952 | 144 |
| N-acetylalanine on A | UNIMOD:1 | 144 |
| Formylation on K | UNIMOD:122 | 138 |
| Acetylation on X | UNIMOD:1 | 118 |
| Phosphorylation on T | UNIMOD:21 | 114 |
| Magnesium on D | UNIMOD:956 | 103 |
| Methylation on R | UNIMOD:34 | 98 |
| Sodium on E | UNIMOD:30 | 96 |
| Carbamyl on K | UNIMOD:5 | 80 |
| Water Loss on E | UNIMOD:27 | 80 |
| Acetylation on K | UNIMOD:1 | 73 |
| Sodium on D | UNIMOD:30 | 71 |
| Dimethylation on K | UNIMOD:36 | 66 |
| Dimethylation on R | UNIMOD:36 | 64 |
| Calcium on E | UNIMOD:951 | 63 |
| N-acetylmethionine on M | UNIMOD:1 | 59 |
| Calcium on D | UNIMOD:951 | 52 |
| N-acetylserine on S | UNIMOD:1 | 50 |
| Carboxylation on E | UNIMOD:299 | 48 |
| HexNAc on S | UNIMOD:43 | 47 |
| N6-acetyllysine on K | UNIMOD:1 | 47 |
| Succinylation on K | UNIMOD:64 | 46 |
| Carboxylation on D | UNIMOD:299 | 45 |
| Crotonylation on K | UNIMOD:1363 | 45 |
| Carboxylation on K | UNIMOD:299 | 44 |
| Hydroxybutyrylation on K | — | 41 |
| Butyrylation on K | UNIMOD:1289 | 36 |
| HexNAc on T | UNIMOD:43 | 35 |
| Malonylation on K | UNIMOD:747 | 30 |
| Potassium on E | UNIMOD:530 | 30 |
| Potassium on D | UNIMOD:530 | 28 |
| Glutarylation on K | UNIMOD:1848 | 27 |
| Trimethylation on K | UNIMOD:37 | 27 |
| Phosphothreonine on T | UNIMOD:21 | 26 |
| Sulfonation on Y | UNIMOD:40 | 26 |
| Cu[I] on E | UNIMOD:531 | 25 |
| Cu[I] on D | UNIMOD:531 | 23 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 20 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 19 |
| Pyridoxal phosphate on K | UNIMOD:46 | 19 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 17 |
| Carbamyl on R | UNIMOD:5 | 17 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 14 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Carbamyl on C | UNIMOD:5 | 13 |
| Carbamyl on M | UNIMOD:5 | 13 |
| Omega-N-methylarginine on R | UNIMOD:34 | 12 |
| ADP-ribosylation on S | UNIMOD:213 | 9 |
| N6-succinyllysine on K | — | 8 |
| Citrulline on R | UNIMOD:7 | 7 |
| N-acetylthreonine on T | UNIMOD:1 | 7 |
| Zinc on E | UNIMOD:954 | 6 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 5 |
| 4-hydroxyproline on P | UNIMOD:35 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
bf8b4970640bcdfc, written 2026-10-29T11:04:30+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