Generated summary
PXD038328 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and runs that differ in enrichment (acetyl on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,397,244 PSMs, 67,381 peptidoforms and 4,719 protein groups, and the repository holds 48,143 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 1.39724e+06 where the producer reported 1.39773e+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 1.39724e+06 where the producer reported 1.39773e+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: 20 run(s) [acetyl]; 20 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: 20 run(s) [acetyl]; 20 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 321185 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 8590 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 321185 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 8590 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: 3171 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: 3171 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: 7 identifier(s), 10 row(s) dropped, e.g. PXD038328:C0HKD1;C0HKD2;C0HKD3;D3YZF6 written 4 times; quant_values: 281 identifier(s), 402 row(s) dropped, e.g. PXD038328:20221108_E1_LS01_Serena_acetylom_A19:label_free:protein_group:PXD038328:C0HKD1;C0HKD2;C0HKD3;D3YZF6:QuantProject:DEF-PROT-SPC written 4 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: 7 identifier(s), 10 row(s) dropped, e.g. PXD038328:C0HKD1;C0HKD2;C0HKD3;D3YZF6 written 4 times; quant_values: 281 identifier(s), 402 row(s) dropped, e.g. PXD038328:20221108_E1_LS01_Serena_acetylom_A19:label_free:protein_group:PXD038328:C0HKD1;C0HKD2;C0HKD3;D3YZF6:QuantProject:DEF-PROT-SPC written 4 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
259 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
259 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 | 1,397,244 |
| Peptidoforms at 1% FDR | 67,381 |
| Protein groups at 1% FDR | 4,719 |
| PTM sites | 48,143 |
| Quantitative values | 1,164,100 |
| PSMs, all (including decoys and sub-threshold) | 2,453,045 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 64.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.5% |
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
- acetyl (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 40 / 40
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2eb9a52d7f0c
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 8,488 |
| Deamidation on Q | UNIMOD:7 | 7,826 |
| Deamidation on N | UNIMOD:7 | 6,242 |
| Oxidation on M | UNIMOD:35 | 5,314 |
| Carbamyl on K | UNIMOD:5 | 2,588 |
| Acetylation on K | UNIMOD:1 | 2,268 |
| Citrullination on R | UNIMOD:7 | 2,135 |
| N6-acetyllysine on K | UNIMOD:1 | 1,636 |
| Hydroxylation on P | UNIMOD:35 | 1,212 |
| Carbamyl on X | UNIMOD:5 | 1,095 |
| Ammonia loss on N | UNIMOD:385 | 749 |
| Hydroxylation on N | UNIMOD:35 | 639 |
| Fe[III] on E | UNIMOD:1870 | 435 |
| Fe[III] on D | UNIMOD:1870 | 392 |
| Magnesium on E | UNIMOD:956 | 358 |
| Sodium on E | UNIMOD:30 | 340 |
| Hydroxylation on K | UNIMOD:35 | 332 |
| Magnesium on D | UNIMOD:956 | 299 |
| Carbamyl on M | UNIMOD:5 | 294 |
| Carboxylation on K | UNIMOD:299 | 279 |
| Sodium on D | UNIMOD:30 | 273 |
| Calcium on E | UNIMOD:951 | 250 |
| Water Loss on E | UNIMOD:27 | 249 |
| Formylation on K | UNIMOD:122 | 239 |
| Calcium on D | UNIMOD:951 | 222 |
| N-acetylalanine on A | UNIMOD:1 | 206 |
| Methylation on K | UNIMOD:34 | 201 |
| Trimethylation on K | UNIMOD:37 | 197 |
| Carboxylation on E | UNIMOD:299 | 171 |
| Fe[II] on E | UNIMOD:952 | 160 |
| Dimethylation on K | UNIMOD:36 | 152 |
| Acetylation on X | UNIMOD:1 | 149 |
| Phosphoserine on S | UNIMOD:21 | 148 |
| Fe[II] on D | UNIMOD:952 | 138 |
| Potassium on E | UNIMOD:530 | 130 |
| Carboxylation on D | UNIMOD:299 | 128 |
| Carbamyl on R | UNIMOD:5 | 106 |
| Ammonia loss on C | UNIMOD:385 | 103 |
| Potassium on D | UNIMOD:530 | 98 |
| N-acetylmethionine on M | UNIMOD:1 | 95 |
| Nitrosylation on Y | UNIMOD:354 | 92 |
| Carbamyl on C | UNIMOD:5 | 86 |
| Methylation on R | UNIMOD:34 | 80 |
| N-acetylserine on S | UNIMOD:1 | 77 |
| Phosphorylation on S | UNIMOD:21 | 67 |
| N6-succinyllysine on K | — | 59 |
| Phosphorylation on T | UNIMOD:21 | 59 |
| Dimethylation on R | UNIMOD:36 | 46 |
| Crotonylation on K | UNIMOD:1363 | 42 |
| Glutarylation on K | UNIMOD:1848 | 40 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 36 |
| Malonylation on K | UNIMOD:747 | 34 |
| Phosphothreonine on T | UNIMOD:21 | 34 |
| 4-hydroxyproline on P | UNIMOD:35 | 33 |
| Butyrylation on K | UNIMOD:1289 | 26 |
| HexNAc on S | UNIMOD:43 | 24 |
| HexNAc on T | UNIMOD:43 | 24 |
| Hydroxybutyrylation on K | — | 24 |
| Nitrosylation on C | UNIMOD:275 | 23 |
| Sulfonation on Y | UNIMOD:40 | 23 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 22 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 22 |
| Succinylation on K | UNIMOD:64 | 22 |
| Cu[I] on E | UNIMOD:531 | 20 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 20 |
| N6-crotonyllysine on K | — | 17 |
| N6-methyllysine on K | UNIMOD:34 | 17 |
| Omega-N-methylarginine on R | UNIMOD:34 | 17 |
| N-acetylthreonine on T | UNIMOD:1 | 16 |
| Cu[I] on D | UNIMOD:531 | 15 |
| Pyridoxal phosphate on K | UNIMOD:46 | 14 |
| N6-glutaryllysine on K | — | 11 |
| Phosphorylation on Y | UNIMOD:21 | 11 |
| Zinc on D | UNIMOD:954 | 8 |
| Zinc on E | UNIMOD:954 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| Dimethylated arginine on R | UNIMOD:36 | 5 |
| N6-butyryllysine on K | UNIMOD:1289 | 5 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 5 |
| N6-methacryllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-acetylproline on P | UNIMOD:1 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| 3'-nitrotyrosine on Y | — | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-malonyllysine on K | — | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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 |
| ADP-ribosylation on S | UNIMOD:213 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Glu to PyroGlu on Q | UNIMOD:28 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| N6-acetyl-N6-methyllysine on K | — | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| Lysino-D-alanine (Lys) on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
a2f27d063aed8c5a, written 2026-10-29T11:51:42+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