Generated summary
PXD057407 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 921,483 PSMs, 29,445 peptidoforms and 4,258 protein groups, and the repository holds 16,734 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 921483 where the producer reported 921655 (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 921483 where the producer reported 921655 (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.
low_core_use warning
12.57 avg cores of 32 allowed (S5)
12.57 avg cores of 32 allowed (S5)
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 13621 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5143 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 13621 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5143 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: 722 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: 722 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), 11 row(s) dropped, e.g. PXD057407:A0A0A6YWK6;A0A0A6YXH1;A0A0A6YXV7;A0A0A6YY61;F6UAK0;F6VPP2;F6X4Y1;F6X518;F6YZA8;F6Z3N5;O88689;Q91Y11;Q91Y13;Q91Y20 written 10 times; quant_values: 20 identifier(s), 110 row(s) dropped, e.g. PXD057407:PPF-RMF-1777-2_Liver_Trypsin_Global_Adult-2_1_A:label_free:protein_group:PXD057407:A0A0A6YWK6;A0A0A6YXH1;A0A0A6YXV7;A0A0A6YY61;F6UAK0;F6VPP2;F6X4Y1;F6X518;F6YZA8;F6Z3N5;O88689;Q91Y11;Q91Y13;Q91Y20:QuantProject:DEF-PROT-SPC written 10 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), 11 row(s) dropped, e.g. PXD057407:A0A0A6YWK6;A0A0A6YXH1;A0A0A6YXV7;A0A0A6YY61;F6UAK0;F6VPP2;F6X4Y1;F6X518;F6YZA8;F6Z3N5;O88689;Q91Y11;Q91Y13;Q91Y20 written 10 times; quant_values: 20 identifier(s), 110 row(s) dropped, e.g. PXD057407:PPF-RMF-1777-2_Liver_Trypsin_Global_Adult-2_1_A:label_free:protein_group:PXD057407:A0A0A6YWK6;A0A0A6YXH1;A0A0A6YXV7;A0A0A6YY61;F6UAK0;F6VPP2;F6X4Y1;F6X518;F6YZA8;F6Z3N5;O88689;Q91Y11;Q91Y13;Q91Y20:QuantProject:DEF-PROT-SPC written 10 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
306 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
306 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 | 921,483 |
| Peptidoforms at 1% FDR | 29,445 |
| Protein groups at 1% FDR | 4,258 |
| PTM sites | 16,734 |
| Quantitative values | 352,449 |
| PSMs, all (including decoys and sub-threshold) | 4,001,628 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 43.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.1% |
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
- 10 / 10
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 852cea5e1cd7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,818 |
| Oxidation on M | UNIMOD:35 | 2,802 |
| Phosphoserine on S | UNIMOD:21 | 322 |
| Hydroxylation on P | UNIMOD:35 | 282 |
| N-acetylalanine on A | UNIMOD:1 | 206 |
| Acetylation on X | UNIMOD:1 | 150 |
| N6-acetyllysine on K | UNIMOD:1 | 141 |
| Phosphorylation on S | UNIMOD:21 | 98 |
| N-acetylmethionine on M | UNIMOD:1 | 92 |
| N-acetylserine on S | UNIMOD:1 | 79 |
| Phosphorylation on T | UNIMOD:21 | 75 |
| 4-hydroxyproline on P | UNIMOD:35 | 53 |
| Phosphothreonine on T | UNIMOD:21 | 53 |
| Omega-N-methylarginine on R | UNIMOD:34 | 48 |
| Acetylation on K | UNIMOD:1 | 42 |
| Methylation on K | UNIMOD:34 | 35 |
| Hydroxylation on K | UNIMOD:35 | 33 |
| N6-succinyllysine on K | — | 24 |
| Dimethylation on K | UNIMOD:36 | 19 |
| HexNAc on T | UNIMOD:43 | 18 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 16 |
| Deamidated asparagine on N | UNIMOD:7 | 16 |
| HexNAc on S | UNIMOD:43 | 16 |
| Phosphotyrosine on Y | UNIMOD:21 | 15 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Trimethylation on K | UNIMOD:37 | 14 |
| Malonylation on K | UNIMOD:747 | 13 |
| Methylation on R | UNIMOD:34 | 12 |
| N-myristoyl glycine on G | UNIMOD:45 | 12 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 12 |
| Crotonylation on K | UNIMOD:1363 | 11 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 11 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 9 |
| Phosphorylation on Y | UNIMOD:21 | 9 |
| Dimethylation on R | UNIMOD:36 | 8 |
| Butyrylation on K | UNIMOD:1289 | 7 |
| Hydroxyproline on P | UNIMOD:35 | 6 |
| Hydroxybutyrylation on K | — | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 4 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| N6-glutaryllysine on K | — | 3 |
| N6-malonyllysine on K | — | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-lipoyllysine on K | UNIMOD:42 | 2 |
| N6-methacryllysine on K | — | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| Pros-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
920efa52d6850a0e, written 2026-10-29T11:20:02+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