Generated summary
PXD077298 is a DDA label-free dataset (Mus musculus) with 22 runs, 22 samples and runs that differ in enrichment (immunoprecipitation and other on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 239,229 PSMs, 37,276 peptidoforms and 4,716 protein groups, and the repository holds 17,144 PTM sites for it. 8 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, 8 warnings and 1 for information
count_mismatch warning
The bundle holds 37277 where the producer reported 37276 (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 37277 where the producer reported 37276 (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 239229 where the producer reported 239250 (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 239229 where the producer reported 239250 (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
54.44% of protein intensity in the worst file, 4.18% median across 22 files (DEF-QC-9 v3.5)
54.44% of protein intensity in the worst file, 4.18% median across 22 files (DEF-QC-9 v3.5)
low_core_use warning
13.67 avg cores of 32 allowed (S5)
13.67 avg cores of 32 allowed (S5)
mixed_enrichment warning
The runs of this dataset differ in enrichment: 8 run(s) [immunoprecipitation]; 8 run(s) [none]; 6 run(s) [other]. 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: 8 run(s) [immunoprecipitation]; 8 run(s) [none]; 6 run(s) [other]. 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 35093 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4629 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 35093 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4629 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: 1307 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: 1307 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
43 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
43 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 | 239,229 |
| Peptidoforms at 1% FDR | 37,276 |
| Protein groups at 1% FDR | 4,716 |
| PTM sites | 17,144 |
| Quantitative values | 361,857 |
| PSMs, all (including decoys and sub-threshold) | 417,446 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 32.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 4.5% |
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
- immunoprecipitation, other (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 22 / 22
- 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 | 7,810 |
| Deamidation on N | UNIMOD:7 | 2,228 |
| Deamidation on Q | UNIMOD:7 | 1,880 |
| Oxidation on M | UNIMOD:35 | 896 |
| Citrullination on R | UNIMOD:7 | 451 |
| Ammonia loss on N | UNIMOD:385 | 304 |
| Hydroxylation on P | UNIMOD:35 | 230 |
| N-acetylalanine on A | UNIMOD:1 | 209 |
| Magnesium on E | UNIMOD:956 | 198 |
| Acetylation on X | UNIMOD:1 | 179 |
| Ammonia loss on C | UNIMOD:385 | 128 |
| Methylation on K | UNIMOD:34 | 128 |
| Phosphoserine on S | UNIMOD:21 | 124 |
| Sodium on E | UNIMOD:30 | 119 |
| N-acetylmethionine on M | UNIMOD:1 | 115 |
| Hydroxylation on N | UNIMOD:35 | 108 |
| Magnesium on D | UNIMOD:956 | 102 |
| Calcium on E | UNIMOD:951 | 90 |
| Hydroxylation on K | UNIMOD:35 | 82 |
| N-acetylserine on S | UNIMOD:1 | 70 |
| Sodium on D | UNIMOD:30 | 60 |
| Water Loss on E | UNIMOD:27 | 60 |
| Carbamyl on X | UNIMOD:5 | 59 |
| Methylation on R | UNIMOD:34 | 56 |
| Phosphorylation on S | UNIMOD:21 | 54 |
| Phosphorylation on T | UNIMOD:21 | 54 |
| Calcium on D | UNIMOD:951 | 52 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 46 |
| Acetylation on K | UNIMOD:1 | 39 |
| Dimethylation on K | UNIMOD:36 | 38 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 35 |
| Phosphothreonine on T | UNIMOD:21 | 35 |
| N6-acetyllysine on K | UNIMOD:1 | 33 |
| Trimethylation on K | UNIMOD:37 | 33 |
| Fe[II] on E | UNIMOD:952 | 29 |
| N-myristoyl glycine on G | UNIMOD:45 | 29 |
| Potassium on D | UNIMOD:530 | 27 |
| Butyrylation on K | UNIMOD:1289 | 25 |
| Crotonylation on K | UNIMOD:1363 | 25 |
| Dimethylation on R | UNIMOD:36 | 25 |
| Fe[III] on D | UNIMOD:1870 | 22 |
| Hydroxybutyrylation on K | — | 21 |
| Potassium on E | UNIMOD:530 | 21 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 20 |
| HexNAc on T | UNIMOD:43 | 20 |
| N-acetylthreonine on T | UNIMOD:1 | 19 |
| Nitrosylation on Y | UNIMOD:354 | 19 |
| Carboxylation on E | UNIMOD:299 | 18 |
| Fe[III] on E | UNIMOD:1870 | 18 |
| Omega-N-methylarginine on R | UNIMOD:34 | 18 |
| Carboxylation on D | UNIMOD:299 | 17 |
| Malonylation on K | UNIMOD:747 | 17 |
| N6-methyllysine on K | UNIMOD:34 | 17 |
| Carbamyl on K | UNIMOD:5 | 15 |
| Deamidated asparagine on N | UNIMOD:7 | 13 |
| HexNAc on S | UNIMOD:43 | 12 |
| Phosphorylation on Y | UNIMOD:21 | 12 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 11 |
| Formylation on K | UNIMOD:122 | 10 |
| Glutarylation on K | UNIMOD:1848 | 10 |
| Carbamyl on M | UNIMOD:5 | 9 |
| Fe[II] on D | UNIMOD:952 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Nitrosylation on C | UNIMOD:275 | 9 |
| Carboxylation on K | UNIMOD:299 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| 3'-nitrotyrosine on Y | — | 5 |
| Carbamyl on C | UNIMOD:5 | 5 |
| Carbamyl on R | UNIMOD:5 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-succinyllysine on K | — | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| Succinylation on K | UNIMOD:64 | 5 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| Sulfonation on Y | UNIMOD:40 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 4-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-methacryllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| S-farnesyl cysteine on C | UNIMOD:44 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 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-butyryllysine on K | UNIMOD:1289 | 1 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 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
9e53e14e120e8541, written 2026-10-29T11:27:26+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