Generated summary
PXD053288 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 660,574 PSMs, 57,685 peptidoforms and 4,947 protein groups, and the repository holds 33,379 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 2 for information
count_mismatch warning
The bundle holds 660574 where the producer reported 660719 (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 660574 where the producer reported 660719 (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.
cysteine_poor warning
1.10% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
1.10% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
low_core_use warning
8.4 avg cores of 32 allowed (S5)
8.4 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 149903 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7072 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 149903 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7072 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: 3236 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: 3236 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), 8 row(s) dropped, e.g. PXD053288:A0A0G2JFY7;A0A0G2JGJ6;G3UXD1;K7N5P5;K7N6W5;L7MU29 written 6 times; quant_values: 48 identifier(s), 96 row(s) dropped, e.g. PXD053288:QEp22-2755_Woo_RYR_H1:label_free:protein_group:PXD053288:A0A0G2JFY7;A0A0G2JGJ6;G3UXD1;K7N5P5;K7N6W5;L7MU29:QuantProject:DEF-PROT-SPC written 6 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), 8 row(s) dropped, e.g. PXD053288:A0A0G2JFY7;A0A0G2JGJ6;G3UXD1;K7N5P5;K7N6W5;L7MU29 written 6 times; quant_values: 48 identifier(s), 96 row(s) dropped, e.g. PXD053288:QEp22-2755_Woo_RYR_H1:label_free:protein_group:PXD053288:A0A0G2JFY7;A0A0G2JGJ6;G3UXD1;K7N5P5;K7N6W5;L7MU29:QuantProject:DEF-PROT-SPC written 6 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
301 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
301 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 | 660,574 |
| Peptidoforms at 1% FDR | 57,685 |
| Protein groups at 1% FDR | 4,947 |
| PTM sites | 33,379 |
| Quantitative values | 609,151 |
| PSMs, all (including decoys and sub-threshold) | 1,193,198 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 75.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.8% |
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
- 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 |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 10,913 |
| Deamidation on Q | UNIMOD:7 | 3,759 |
| Deamidation on N | UNIMOD:7 | 3,548 |
| Hydroxylation on P | UNIMOD:35 | 1,365 |
| Carbamyl on X | UNIMOD:5 | 1,243 |
| Fe[II] on E | UNIMOD:952 | 1,030 |
| Fe[II] on D | UNIMOD:952 | 995 |
| Methylthio on C | UNIMOD:39 | 904 |
| Fe[III] on E | UNIMOD:1870 | 852 |
| Fe[III] on D | UNIMOD:1870 | 767 |
| Citrullination on R | UNIMOD:7 | 717 |
| Ammonia loss on N | UNIMOD:385 | 672 |
| Hydroxylation on N | UNIMOD:35 | 664 |
| Hydroxylation on K | UNIMOD:35 | 465 |
| Phosphoserine on S | UNIMOD:21 | 434 |
| Methylation on K | UNIMOD:34 | 332 |
| Sodium on E | UNIMOD:30 | 285 |
| Sodium on D | UNIMOD:30 | 272 |
| N-acetylalanine on A | UNIMOD:1 | 232 |
| Dimethylation on K | UNIMOD:36 | 220 |
| Phosphorylation on S | UNIMOD:21 | 215 |
| Acetylation on X | UNIMOD:1 | 201 |
| Phosphorylation on T | UNIMOD:21 | 159 |
| Carbamyl on K | UNIMOD:5 | 147 |
| Magnesium on E | UNIMOD:956 | 142 |
| Dimethylation on R | UNIMOD:36 | 136 |
| Methylation on R | UNIMOD:34 | 124 |
| Magnesium on D | UNIMOD:956 | 118 |
| Calcium on E | UNIMOD:951 | 117 |
| Acetylation on K | UNIMOD:1 | 109 |
| Calcium on D | UNIMOD:951 | 103 |
| Phosphothreonine on T | UNIMOD:21 | 90 |
| N-acetylserine on S | UNIMOD:1 | 80 |
| N-acetylmethionine on M | UNIMOD:1 | 76 |
| N6-acetyllysine on K | UNIMOD:1 | 74 |
| Water Loss on E | UNIMOD:27 | 71 |
| Carbamyl on M | UNIMOD:5 | 66 |
| Carboxylation on D | UNIMOD:299 | 61 |
| HexNAc on T | UNIMOD:43 | 59 |
| Carboxylation on E | UNIMOD:299 | 55 |
| Trimethylation on K | UNIMOD:37 | 54 |
| HexNAc on S | UNIMOD:43 | 51 |
| Potassium on E | UNIMOD:530 | 45 |
| Formylation on K | UNIMOD:122 | 41 |
| Potassium on D | UNIMOD:530 | 41 |
| Carbamyl on R | UNIMOD:5 | 34 |
| Sulfonation on Y | UNIMOD:40 | 32 |
| Carbamyl on C | UNIMOD:5 | 31 |
| Omega-N-methylarginine on R | UNIMOD:34 | 31 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 27 |
| Malonylation on K | UNIMOD:747 | 27 |
| Hydroxybutyrylation on K | — | 25 |
| Phosphorylation on Y | UNIMOD:21 | 25 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 23 |
| Crotonylation on K | UNIMOD:1363 | 21 |
| N-acetylthreonine on T | UNIMOD:1 | 20 |
| N6-succinyllysine on K | — | 20 |
| Butyrylation on K | UNIMOD:1289 | 18 |
| Glutarylation on K | UNIMOD:1848 | 18 |
| 4-hydroxyproline on P | UNIMOD:35 | 17 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 17 |
| Nitrosylation on Y | UNIMOD:354 | 17 |
| Succinylation on K | UNIMOD:64 | 16 |
| Deamidated asparagine on N | UNIMOD:7 | 14 |
| N-myristoyl glycine on G | UNIMOD:45 | 13 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 12 |
| N6-methyllysine on K | UNIMOD:34 | 11 |
| Carboxylation on K | UNIMOD:299 | 10 |
| Phosphotyrosine on Y | UNIMOD:21 | 10 |
| Nitrosylation on C | UNIMOD:275 | 9 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| Pyridoxal phosphate on K | UNIMOD:46 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-glutaryllysine on K | — | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| Phosphohistidine on H | UNIMOD:21 | 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
ff52ec0c4aca854f, written 2026-10-29T09:49:18+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