Generated summary
PXD061654 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and runs that differ in enrichment (acetyl on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 2,789,721 PSMs, 55,792 peptidoforms and 3,866 protein groups, and the repository holds 36,045 PTM sites for it. 6 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, 6 warnings and 1 for information
count_mismatch warning
The bundle holds 2.78972e+06 where the producer reported 2.7906e+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 2.78972e+06 where the producer reported 2.7906e+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.
mixed_enrichment warning
The runs of this dataset differ in enrichment: 18 run(s) [acetyl]; 12 run(s) [none]. The dataset's own `enrichment` is the producer's declaration and is true of only some runs, so answer any enrichment-dependent question per run from `runs.enrichment`, and never pool its runs as one kind.
The runs of this dataset differ in enrichment: 18 run(s) [acetyl]; 12 run(s) [none]. The dataset's own `enrichment` is the producer's declaration and is true of only some runs, so answer any enrichment-dependent question per run from `runs.enrichment`, and never pool its runs as one kind.
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 649898 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 14562 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 649898 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 14562 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
1342 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 5103 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. `AAAHHYGAQC[Common Fixed:Carbamidomethyl on C]DKTNK[Common Biological:Acetylation on K]EFMLC[Common Fixed:Carbamidomethyl on C]R|AAAHHYGAQC[Common Fixed:Carbamidomethyl on C]DK[Common Biological:Acetylation on K]TNKEFMLC[Common Fixed:Carbamidomethyl on C]R`, `AADAHVDAHYYEQNE[Metal:Fe[II] on E]QPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR|AADAHVDAHYYE[Metal:Fe[II] on E]QNEQPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR`, `AADEVAEGK[Common Biological:Methylation on K]LNDHFPLVVWQTGSGTQTN[Common Artifact:Deamidation on N]MNVNEVISNR|AADEVAEGK[Common Biological:Methylation on K]LNDHFPLVVWQTGSGTQ[Common Artifact:Deamidation on Q]TNMNVNEVISNR`.
1342 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 5103 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. `AAAHHYGAQC[Common Fixed:Carbamidomethyl on C]DKTNK[Common Biological:Acetylation on K]EFMLC[Common Fixed:Carbamidomethyl on C]R|AAAHHYGAQC[Common Fixed:Carbamidomethyl on C]DK[Common Biological:Acetylation on K]TNKEFMLC[Common Fixed:Carbamidomethyl on C]R`, `AADAHVDAHYYEQNE[Metal:Fe[II] on E]QPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR|AADAHVDAHYYE[Metal:Fe[II] on E]QNEQPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR`, `AADEVAEGK[Common Biological:Methylation on K]LNDHFPLVVWQTGSGTQTN[Common Artifact:Deamidation on N]MNVNEVISNR|AADEVAEGK[Common Biological:Methylation on K]LNDHFPLVVWQTGSGTQ[Common Artifact:Deamidation on Q]TNMNVNEVISNR`.
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: 10117 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: 10117 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
73 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
73 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 | 2,789,721 |
| Peptidoforms at 1% FDR | 55,792 |
| Protein groups at 1% FDR | 3,866 |
| PTM sites | 36,045 |
| Quantitative values | 1,074,279 |
| PSMs, all (including decoys and sub-threshold) | 6,939,246 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 59.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
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
- acetyl (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 30 / 30
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v6.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 10,553 |
| Oxidation on M | UNIMOD:35 | 6,651 |
| Acetylation on K | UNIMOD:1 | 4,731 |
| Carbamyl on K | UNIMOD:5 | 2,125 |
| N6-acetyllysine on K | UNIMOD:1 | 2,011 |
| Carbamyl on X | UNIMOD:5 | 1,238 |
| Deamidation on N | UNIMOD:7 | 425 |
| Deamidation on Q | UNIMOD:7 | 410 |
| Methylation on K | UNIMOD:34 | 403 |
| Sodium on E | UNIMOD:30 | 347 |
| Sodium on D | UNIMOD:30 | 313 |
| N-acetylalanine on A | UNIMOD:1 | 300 |
| Trimethylation on K | UNIMOD:37 | 295 |
| Acetylation on X | UNIMOD:1 | 285 |
| Hydroxylation on P | UNIMOD:35 | 261 |
| Phosphoserine on S | UNIMOD:21 | 246 |
| Fe[III] on E | UNIMOD:1870 | 240 |
| Carbamyl on M | UNIMOD:5 | 233 |
| Fe[II] on E | UNIMOD:952 | 209 |
| Fe[III] on D | UNIMOD:1870 | 200 |
| Hydroxylation on K | UNIMOD:35 | 180 |
| Ammonia loss on C | UNIMOD:385 | 178 |
| Formylation on K | UNIMOD:122 | 164 |
| Fe[II] on D | UNIMOD:952 | 160 |
| Ammonia loss on N | UNIMOD:385 | 147 |
| Dimethylation on K | UNIMOD:36 | 144 |
| Methylation on R | UNIMOD:34 | 144 |
| Hydroxylation on N | UNIMOD:35 | 140 |
| Magnesium on E | UNIMOD:956 | 134 |
| Citrullination on R | UNIMOD:7 | 117 |
| Calcium on E | UNIMOD:951 | 116 |
| N6-succinyllysine on K | — | 116 |
| Calcium on D | UNIMOD:951 | 114 |
| Phosphorylation on S | UNIMOD:21 | 112 |
| Carbamyl on R | UNIMOD:5 | 110 |
| N-acetylserine on S | UNIMOD:1 | 108 |
| Magnesium on D | UNIMOD:956 | 107 |
| N-acetylmethionine on M | UNIMOD:1 | 106 |
| Malonylation on K | UNIMOD:747 | 100 |
| HexNAc on S | UNIMOD:43 | 96 |
| HexNAc on T | UNIMOD:43 | 94 |
| Water Loss on E | UNIMOD:27 | 86 |
| Butyrylation on K | UNIMOD:1289 | 80 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 80 |
| Crotonylation on K | UNIMOD:1363 | 76 |
| Phosphorylation on T | UNIMOD:21 | 76 |
| Phosphothreonine on T | UNIMOD:21 | 72 |
| Hydroxybutyrylation on K | — | 71 |
| Dimethylation on R | UNIMOD:36 | 62 |
| 4-hydroxyproline on P | UNIMOD:35 | 56 |
| Succinylation on K | UNIMOD:64 | 56 |
| Glutarylation on K | UNIMOD:1848 | 53 |
| Carbamyl on C | UNIMOD:5 | 49 |
| Omega-N-methylarginine on R | UNIMOD:34 | 48 |
| Potassium on D | UNIMOD:530 | 44 |
| Carboxylation on K | UNIMOD:299 | 43 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 43 |
| N6-glutaryllysine on K | — | 36 |
| Potassium on E | UNIMOD:530 | 36 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 33 |
| N6-methyllysine on K | UNIMOD:34 | 33 |
| N6-crotonyllysine on K | — | 29 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 27 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 27 |
| Nitrosylation on C | UNIMOD:275 | 27 |
| N-acetylthreonine on T | UNIMOD:1 | 26 |
| Phosphorylation on Y | UNIMOD:21 | 21 |
| Carboxylation on E | UNIMOD:299 | 20 |
| Carboxylation on D | UNIMOD:299 | 18 |
| Deamidated asparagine on N | UNIMOD:7 | 17 |
| N6-benzoyllysine on K | UNIMOD:136 | 16 |
| Nitrosylation on Y | UNIMOD:354 | 13 |
| Phosphotyrosine on Y | UNIMOD:21 | 12 |
| N-myristoyl glycine on G | UNIMOD:45 | 10 |
| N6-butyryllysine on K | UNIMOD:1289 | 10 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 10 |
| N6-methacryllysine on K | — | 9 |
| Citrulline on R | UNIMOD:7 | 8 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 7 |
| N5-methylglutamine on Q | UNIMOD:34 | 7 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 7 |
| 5-hydroxylysine on K | UNIMOD:35 | 6 |
| Methionine (R)-sulfoxide on M | UNIMOD:35 | 6 |
| Pros-methylhistidine on H | UNIMOD:34 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 6 |
| Zinc on D | UNIMOD:954 | 6 |
| Allysine on K | UNIMOD:352 | 5 |
| N6-malonyllysine on K | — | 5 |
| 3-hydroxyproline on P | UNIMOD:35 | 4 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Glu to PyroGlu on Q | UNIMOD:28 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 4 |
| Cu[I] on E | UNIMOD:531 | 3 |
| N-acetylproline on P | UNIMOD:1 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| N6-acetyl-N6-methyllysine on K | — | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-glutamyl dopamine on Q | — | 1 |
| 5-glutamyl serotonin on Q | — | 1 |
| Cu[I] on D | UNIMOD:531 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| Phosphoarginine on R | UNIMOD:21 | 1 |
| Pyridoxal phosphate on K | UNIMOD:46 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
cd8c7dea288dba6e, written 2026-10-30T05:47:44+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