Generated summary
PXD025321 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 771,808 PSMs, 55,484 peptidoforms and 4,351 protein groups, and the repository holds 27,803 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 771808 where the producer reported 771996 (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 771808 where the producer reported 771996 (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 75425 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 8952 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 75425 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 8952 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: 6054 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: 6054 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), 1 row(s) dropped, e.g. PXD025321:A0ABJ3HPE9;B1AT01 written 2 times; quant_values: 15 identifier(s), 15 row(s) dropped, e.g. PXD025321:AmAc-24hr-1:label_free:protein_group:PXD025321:A0ABJ3HPE9;B1AT01: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: 1 identifier(s), 1 row(s) dropped, e.g. PXD025321:A0ABJ3HPE9;B1AT01 written 2 times; quant_values: 15 identifier(s), 15 row(s) dropped, e.g. PXD025321:AmAc-24hr-1:label_free:protein_group:PXD025321:A0ABJ3HPE9;B1AT01:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
100 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
100 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 | 771,808 |
| Peptidoforms at 1% FDR | 55,484 |
| Protein groups at 1% FDR | 4,351 |
| PTM sites | 27,803 |
| Quantitative values | 520,569 |
| PSMs, all (including decoys and sub-threshold) | 1,134,432 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 61.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.4% |
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
- 15 / 15
- 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 | 11,136 |
| Deamidation on Q | UNIMOD:7 | 2,135 |
| Oxidation on M | UNIMOD:35 | 2,120 |
| Deamidation on N | UNIMOD:7 | 1,697 |
| Calcium on E | UNIMOD:951 | 858 |
| Ammonia loss on N | UNIMOD:385 | 709 |
| Hydroxylation on P | UNIMOD:35 | 685 |
| Sodium on E | UNIMOD:30 | 630 |
| Calcium on D | UNIMOD:951 | 558 |
| Citrullination on R | UNIMOD:7 | 471 |
| Sodium on D | UNIMOD:30 | 450 |
| Magnesium on E | UNIMOD:956 | 421 |
| Ammonia loss on C | UNIMOD:385 | 314 |
| N-acetylalanine on A | UNIMOD:1 | 299 |
| Hydroxylation on K | UNIMOD:35 | 293 |
| Carbamyl on X | UNIMOD:5 | 281 |
| Magnesium on D | UNIMOD:956 | 275 |
| Acetylation on X | UNIMOD:1 | 252 |
| Methylation on K | UNIMOD:34 | 243 |
| Phosphoserine on S | UNIMOD:21 | 240 |
| Hydroxylation on N | UNIMOD:35 | 233 |
| Potassium on E | UNIMOD:530 | 225 |
| Potassium on D | UNIMOD:530 | 174 |
| Phosphorylation on S | UNIMOD:21 | 167 |
| N-acetylmethionine on M | UNIMOD:1 | 161 |
| Carbamyl on K | UNIMOD:5 | 144 |
| Water Loss on E | UNIMOD:27 | 136 |
| Acetylation on K | UNIMOD:1 | 120 |
| N-acetylserine on S | UNIMOD:1 | 109 |
| Carbamyl on M | UNIMOD:5 | 102 |
| Dimethylation on K | UNIMOD:36 | 99 |
| Methylation on R | UNIMOD:34 | 91 |
| N6-acetyllysine on K | UNIMOD:1 | 90 |
| Phosphorylation on T | UNIMOD:21 | 81 |
| Trimethylation on K | UNIMOD:37 | 74 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 73 |
| 4-hydroxyproline on P | UNIMOD:35 | 71 |
| HexNAc on S | UNIMOD:43 | 62 |
| Dimethylation on R | UNIMOD:36 | 58 |
| Butyrylation on K | UNIMOD:1289 | 57 |
| Crotonylation on K | UNIMOD:1363 | 54 |
| Fe[III] on E | UNIMOD:1870 | 51 |
| Glutarylation on K | UNIMOD:1848 | 50 |
| HexNAc on T | UNIMOD:43 | 50 |
| Fe[II] on E | UNIMOD:952 | 46 |
| Phosphothreonine on T | UNIMOD:21 | 46 |
| Malonylation on K | UNIMOD:747 | 42 |
| Fe[III] on D | UNIMOD:1870 | 37 |
| Fe[II] on D | UNIMOD:952 | 36 |
| Hydroxybutyrylation on K | — | 35 |
| Omega-N-methylarginine on R | UNIMOD:34 | 34 |
| Formylation on K | UNIMOD:122 | 32 |
| N-acetylthreonine on T | UNIMOD:1 | 30 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 23 |
| Nitrosylation on Y | UNIMOD:354 | 23 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 22 |
| Phosphorylation on Y | UNIMOD:21 | 22 |
| Succinylation on K | UNIMOD:64 | 21 |
| Carbamyl on R | UNIMOD:5 | 20 |
| Cu[I] on E | UNIMOD:531 | 19 |
| N6-succinyllysine on K | — | 19 |
| Pyridoxal phosphate on K | UNIMOD:46 | 19 |
| Carbamyl on C | UNIMOD:5 | 17 |
| N-myristoyl glycine on G | UNIMOD:45 | 16 |
| N6-methyllysine on K | UNIMOD:34 | 15 |
| Carboxylation on E | UNIMOD:299 | 14 |
| Nitrosylation on C | UNIMOD:275 | 14 |
| Cu[I] on D | UNIMOD:531 | 13 |
| N6-glutaryllysine on K | — | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| Sulfonation on Y | UNIMOD:40 | 12 |
| Carboxylation on D | UNIMOD:299 | 11 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| ADP-ribosylation on S | UNIMOD:213 | 7 |
| N-acetylcysteine on C | UNIMOD:1 | 7 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| N6-crotonyllysine on K | — | 6 |
| Pros-methylhistidine on H | UNIMOD:34 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 6 |
| 3-hydroxyproline on P | UNIMOD:35 | 5 |
| Carboxylation on K | UNIMOD:299 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Allysine on K | UNIMOD:352 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| N6-malonyllysine on K | — | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxylysine on K | — | 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 Nxt | UNIMOD:43 | 1 |
| N,N,N-trimethylalanine on A | UNIMOD:37 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-methacryllysine on K | — | 1 |
| S-(2,3-dicarboxypropyl)cysteine on C | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
418b321081347dd4, written 2026-10-29T09:42:03+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