Generated summary
PXD018097 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and runs that differ in enrichment (phospho on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 762,720 PSMs, 101,119 peptidoforms and 8,079 protein groups, and the repository holds 52,657 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 2 for information
count_mismatch warning
The bundle holds 762720 where the producer reported 762818 (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 762720 where the producer reported 762818 (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
4.03 avg cores of 32 allowed (S5)
4.03 avg cores of 32 allowed (S5)
mixed_enrichment warning
The runs of this dataset differ in enrichment: 6 run(s) [none]; 6 run(s) [phospho]. 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: 6 run(s) [none]; 6 run(s) [phospho]. 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 185643 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 7448 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 185643 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 7448 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).
spectral_library warning
mouse's current library moved from version 102 to 103 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD018097\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-26-01-01-23.msp and has NOT been registered, so nothing was lost; merge it deliberately.
mouse's current library moved from version 102 to 103 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD018097\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-26-01-01-23.msp and has NOT been registered, so nothing was lost; merge it deliberately.
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: 781 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: 781 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: 4 identifier(s), 11 row(s) dropped, e.g. PXD018097:A0A6B9UF22;A0A9L6KE92 written 2 times; quant_values: 50 identifier(s), 134 row(s) dropped, e.g. PXD018097:20190404_HN_0018_HaSp_ColID_456_DDA_sample_01:label_free:protein_group:PXD018097:A0A6B9UF22;A0A9L6KE92:QuantProject:DEF-PROT-INT written 2 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: 4 identifier(s), 11 row(s) dropped, e.g. PXD018097:A0A6B9UF22;A0A9L6KE92 written 2 times; quant_values: 50 identifier(s), 134 row(s) dropped, e.g. PXD018097:20190404_HN_0018_HaSp_ColID_456_DDA_sample_01:label_free:protein_group:PXD018097:A0A6B9UF22;A0A9L6KE92:QuantProject:DEF-PROT-INT written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
72 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
72 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 | 762,720 |
| Peptidoforms at 1% FDR | 101,119 |
| Protein groups at 1% FDR | 8,079 |
| PTM sites | 52,657 |
| Quantitative values | 591,188 |
| PSMs, all (including decoys and sub-threshold) | 1,278,290 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 79.8% |
| 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
- phospho (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 12 / 12
- 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 | 18,459 |
| Phosphorylation on S | UNIMOD:21 | 7,263 |
| Phosphoserine on S | UNIMOD:21 | 6,648 |
| Deamidation on N | UNIMOD:7 | 3,899 |
| Oxidation on M | UNIMOD:35 | 2,770 |
| Deamidation on Q | UNIMOD:7 | 2,250 |
| Phosphorylation on T | UNIMOD:21 | 1,957 |
| Ammonia loss on N | UNIMOD:385 | 981 |
| Phosphothreonine on T | UNIMOD:21 | 723 |
| Hydroxylation on P | UNIMOD:35 | 639 |
| Citrullination on R | UNIMOD:7 | 530 |
| Ammonia loss on C | UNIMOD:385 | 457 |
| Phosphorylation on Y | UNIMOD:21 | 431 |
| Acetylation on X | UNIMOD:1 | 414 |
| Sulfonation on Y | UNIMOD:40 | 374 |
| Water Loss on E | UNIMOD:27 | 369 |
| N-acetylalanine on A | UNIMOD:1 | 361 |
| Sodium on E | UNIMOD:30 | 319 |
| Sodium on D | UNIMOD:30 | 246 |
| N-acetylmethionine on M | UNIMOD:1 | 214 |
| Magnesium on E | UNIMOD:956 | 208 |
| Magnesium on D | UNIMOD:956 | 184 |
| Formylation on K | UNIMOD:122 | 178 |
| Calcium on E | UNIMOD:951 | 155 |
| N-acetylserine on S | UNIMOD:1 | 137 |
| N6-acetyllysine on K | UNIMOD:1 | 131 |
| Calcium on D | UNIMOD:951 | 125 |
| Hydroxylation on N | UNIMOD:35 | 105 |
| Carbamyl on X | UNIMOD:5 | 104 |
| Omega-N-methylarginine on R | UNIMOD:34 | 88 |
| Hydroxylation on K | UNIMOD:35 | 84 |
| 4-hydroxyproline on P | UNIMOD:35 | 78 |
| Methylation on K | UNIMOD:34 | 77 |
| HexNAc on T | UNIMOD:43 | 74 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 71 |
| Potassium on E | UNIMOD:530 | 67 |
| Dimethylation on R | UNIMOD:36 | 64 |
| Phosphotyrosine on Y | UNIMOD:21 | 61 |
| Acetylation on K | UNIMOD:1 | 59 |
| HexNAc on S | UNIMOD:43 | 49 |
| Potassium on D | UNIMOD:530 | 44 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 43 |
| Dimethylation on K | UNIMOD:36 | 36 |
| Methylation on R | UNIMOD:34 | 36 |
| Fe[III] on D | UNIMOD:1870 | 35 |
| N6-methyllysine on K | UNIMOD:34 | 34 |
| Fe[II] on D | UNIMOD:952 | 33 |
| Pyridoxal phosphate on K | UNIMOD:46 | 33 |
| Fe[II] on E | UNIMOD:952 | 32 |
| Fe[III] on E | UNIMOD:1870 | 31 |
| Crotonylation on K | UNIMOD:1363 | 29 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 29 |
| Carboxylation on D | UNIMOD:299 | 28 |
| N-acetylthreonine on T | UNIMOD:1 | 28 |
| Trimethylation on K | UNIMOD:37 | 26 |
| Butyrylation on K | UNIMOD:1289 | 24 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 24 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 23 |
| Cu[I] on E | UNIMOD:531 | 21 |
| Cu[I] on D | UNIMOD:531 | 19 |
| N6-crotonyllysine on K | — | 18 |
| Carboxylation on K | UNIMOD:299 | 16 |
| Malonylation on K | UNIMOD:747 | 16 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| N-myristoyl glycine on G | UNIMOD:45 | 15 |
| N6-succinyllysine on K | — | 15 |
| Carboxylation on E | UNIMOD:299 | 14 |
| Glutarylation on K | UNIMOD:1848 | 13 |
| N-acetylglycine on G | UNIMOD:1 | 12 |
| Succinylation on K | UNIMOD:64 | 12 |
| Carbamyl on M | UNIMOD:5 | 10 |
| ADP-ribosylation on S | UNIMOD:213 | 8 |
| Nitrosylation on C | UNIMOD:275 | 8 |
| N6-butyryllysine on K | UNIMOD:1289 | 7 |
| Carbamyl on K | UNIMOD:5 | 6 |
| Dimethylated arginine on R | UNIMOD:36 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N5-methylglutamine on Q | UNIMOD:34 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Pros-methylhistidine on H | UNIMOD:34 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Zinc on E | UNIMOD:954 | 4 |
| ADP-ribosylserine on S | UNIMOD:213 | 3 |
| Carbamyl on R | UNIMOD:5 | 3 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| Hydroxybutyrylation on K | — | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 3 |
| S-farnesyl cysteine on C | UNIMOD:44 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| (3S)-3-hydroxylysine on K | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| N6-acetyl-N6-methyllysine on K | — | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 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
c49c3f793175ae48, written 2026-10-29T09:20:54+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