Generated summary
PXD026934 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 904,188 PSMs, 83,886 peptidoforms and 7,573 protein groups, and the repository holds 24,351 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 904188 where the producer reported 904190 (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 904188 where the producer reported 904190 (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
13.49 avg cores of 32 allowed (S5)
13.49 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 61984 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3778 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 61984 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3778 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: 1200 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: 1200 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD026934:A0A088MLT8;P0DPB4 written 2 times; quant_values: 43 identifier(s), 43 row(s) dropped, e.g. PXD026934:20210324_E1_LC6col188_TB_Chrysanthi_intestinal_cells_843:label_free:protein_group:PXD026934:A0A088MLT8;P0DPB4:QuantProject:DEF-PROT-SPC 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD026934:A0A088MLT8;P0DPB4 written 2 times; quant_values: 43 identifier(s), 43 row(s) dropped, e.g. PXD026934:20210324_E1_LC6col188_TB_Chrysanthi_intestinal_cells_843:label_free:protein_group:PXD026934:A0A088MLT8;P0DPB4:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
38 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
38 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 | 904,188 |
| Peptidoforms at 1% FDR | 83,886 |
| Protein groups at 1% FDR | 7,573 |
| PTM sites | 24,351 |
| Quantitative values | 1,045,169 |
| PSMs, all (including decoys and sub-threshold) | 1,124,603 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 57.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.4% |
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
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0bf698d2cd0a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,980 |
| Oxidation on M | UNIMOD:35 | 4,360 |
| Deamidation on Q | UNIMOD:7 | 2,166 |
| Deamidation on N | UNIMOD:7 | 1,955 |
| Citrullination on R | UNIMOD:7 | 478 |
| Carbamyl on X | UNIMOD:5 | 456 |
| Water Loss on E | UNIMOD:27 | 334 |
| Ammonia loss on N | UNIMOD:385 | 317 |
| Phosphoserine on S | UNIMOD:21 | 312 |
| Hydroxylation on P | UNIMOD:35 | 242 |
| Ammonia loss on C | UNIMOD:385 | 105 |
| Phosphorylation on S | UNIMOD:21 | 101 |
| Hydroxylation on N | UNIMOD:35 | 99 |
| N-acetylalanine on A | UNIMOD:1 | 92 |
| Acetylation on X | UNIMOD:1 | 88 |
| Hydroxylation on K | UNIMOD:35 | 60 |
| Carbamyl on K | UNIMOD:5 | 57 |
| Formylation on K | UNIMOD:122 | 56 |
| N-acetylmethionine on M | UNIMOD:1 | 52 |
| N-acetylserine on S | UNIMOD:1 | 52 |
| Phosphorylation on T | UNIMOD:21 | 51 |
| N6-acetyllysine on K | UNIMOD:1 | 40 |
| HexNAc on S | UNIMOD:43 | 35 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 30 |
| HexNAc on T | UNIMOD:43 | 30 |
| Omega-N-methylarginine on R | UNIMOD:34 | 29 |
| Phosphothreonine on T | UNIMOD:21 | 28 |
| Sodium on D | UNIMOD:30 | 27 |
| Phosphorylation on Y | UNIMOD:21 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 19 |
| Acetylation on K | UNIMOD:1 | 17 |
| Succinylation on K | UNIMOD:64 | 17 |
| Carbamyl on R | UNIMOD:5 | 16 |
| Methylation on K | UNIMOD:34 | 16 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 15 |
| Dimethylation on R | UNIMOD:36 | 14 |
| Sodium on E | UNIMOD:30 | 14 |
| Magnesium on D | UNIMOD:956 | 13 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 12 |
| N6-methyllysine on K | UNIMOD:34 | 12 |
| HexNAc on Nxs | UNIMOD:43 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 10 |
| Sulfonation on Y | UNIMOD:40 | 10 |
| Deamidated asparagine on N | UNIMOD:7 | 9 |
| HexNAc on Nxt | UNIMOD:43 | 8 |
| Methylation on R | UNIMOD:34 | 8 |
| N-myristoyl glycine on G | UNIMOD:45 | 8 |
| Phosphotyrosine on Y | UNIMOD:21 | 8 |
| Magnesium on E | UNIMOD:956 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 6 |
| Carbamyl on M | UNIMOD:5 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 5 |
| N6-succinyllysine on K | — | 5 |
| Dimethylation on K | UNIMOD:36 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Trimethylation on K | UNIMOD:37 | 4 |
| Carbamyl on C | UNIMOD:5 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 4-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Glu to PyroGlu on Q | UNIMOD:28 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
55da80cfc3f3c8c7, written 2026-10-29T09:55:16+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