Generated summary
PXD027526 is a DDA label-free dataset (Mus musculus) with 153 runs, 153 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 643,119 PSMs, 47,450 peptidoforms and 6,953 protein groups, and the repository holds 23,757 PTM sites for it. 7 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, 7 warnings and 1 for information
count_mismatch warning
The bundle holds 47451 where the producer reported 47450 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 47451 where the producer reported 47450 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
count_mismatch warning
The bundle holds 643119 where the producer reported 643194 (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 643119 where the producer reported 643194 (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
2.28 avg cores of 32 allowed (S5)
2.28 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 84503 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11828 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 84503 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11828 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).
peptide_rows_localization_ambiguous warning
79 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 188 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `ADTPGEAT[Common Biological:HexNAc on T]PPPRK|ADT[Common Biological:HexNAc on T]PGEATPPPRK`, `AGEVINQPMMM[Common Variable:Oxidation on M]AAR|AGEVINQPMM[Common Variable:Oxidation on M]MAAR`, `AGEVINQPM[Common Variable:Oxidation on M]MM[Common Variable:Oxidation on M]AAR|AGEVINQPM[Common Variable:Oxidation on M]M[Common Variable:Oxidation on M]MAAR`.
79 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 188 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `ADTPGEAT[Common Biological:HexNAc on T]PPPRK|ADT[Common Biological:HexNAc on T]PGEATPPPRK`, `AGEVINQPMMM[Common Variable:Oxidation on M]AAR|AGEVINQPMM[Common Variable:Oxidation on M]MAAR`, `AGEVINQPM[Common Variable:Oxidation on M]MM[Common Variable:Oxidation on M]AAR|AGEVINQPM[Common Variable:Oxidation on M]M[Common Variable:Oxidation on M]MAAR`.
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: 604 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: 604 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.
occupancy_decoy_groups info
198 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
198 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 | 643,119 |
| Peptidoforms at 1% FDR | 47,450 |
| Protein groups at 1% FDR | 6,953 |
| PTM sites | 23,757 |
| Quantitative values | 2,291,153 |
| PSMs, all (including decoys and sub-threshold) | 5,176,846 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 16.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.6% |
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
- 153 / 153
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 10,777 |
| Carbamidomethyl on C | UNIMOD:4 | 9,948 |
| Phosphoserine on S | UNIMOD:21 | 589 |
| Hydroxylation on P | UNIMOD:35 | 444 |
| N-acetylalanine on A | UNIMOD:1 | 245 |
| Acetylation on X | UNIMOD:1 | 189 |
| N-acetylmethionine on M | UNIMOD:1 | 144 |
| Phosphorylation on S | UNIMOD:21 | 141 |
| N6-acetyllysine on K | UNIMOD:1 | 137 |
| N-acetylserine on S | UNIMOD:1 | 105 |
| Phosphorylation on T | UNIMOD:21 | 97 |
| Omega-N-methylarginine on R | UNIMOD:34 | 91 |
| Phosphothreonine on T | UNIMOD:21 | 87 |
| 4-hydroxyproline on P | UNIMOD:35 | 80 |
| Hydroxylation on K | UNIMOD:35 | 70 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 56 |
| Acetylation on K | UNIMOD:1 | 35 |
| N6-succinyllysine on K | — | 29 |
| Methylation on K | UNIMOD:34 | 25 |
| HexNAc on S | UNIMOD:43 | 23 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 21 |
| N-acetylthreonine on T | UNIMOD:1 | 21 |
| HexNAc on T | UNIMOD:43 | 19 |
| Phosphorylation on Y | UNIMOD:21 | 18 |
| Phosphotyrosine on Y | UNIMOD:21 | 18 |
| Methylation on R | UNIMOD:34 | 17 |
| Dimethylation on R | UNIMOD:36 | 16 |
| N6-glutaryllysine on K | — | 15 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| Dimethylation on K | UNIMOD:36 | 11 |
| N-myristoyl glycine on G | UNIMOD:45 | 11 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| Malonylation on K | UNIMOD:747 | 8 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| Trimethylation on K | UNIMOD:37 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-benzoyllysine on K | UNIMOD:136 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 4 |
| Hydroxyproline on P | UNIMOD:35 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| 3'-nitrotyrosine on Y | — | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| N6-crotonyllysine on K | — | 3 |
| N6-methacryllysine on K | — | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| (3S)-3-hydroxylysine on K | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 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-acetyl-N6-methyllysine on K | — | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| N6-malonyllysine on K | — | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
6becff369a171df6, written 2026-11-01T10:15:01+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group