Generated summary
PXD025503 is a DDA label-free dataset (Mus musculus) with 9 runs, 9 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 521,289 PSMs, 67,071 peptidoforms and 4,656 protein groups, and the repository holds 34,371 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 521289 where the producer reported 521636 (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 521289 where the producer reported 521636 (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
5.04 avg cores of 32 allowed (S5)
5.04 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 79190 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 duplicate entry for one site and run (identical values; same protein group); 5278 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 79190 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 duplicate entry for one site and run (identical values; same protein group); 5278 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: 1340 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: 1340 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. PXD025503:F8VPQ6;P24822 written 2 times; quant_values: 18 identifier(s), 18 row(s) dropped, e.g. PXD025503:20200716_Q2_UC_ColID_938_ProjID_2165_Trifunovic_1:label_free:protein_group:PXD025503:F8VPQ6;P24822: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. PXD025503:F8VPQ6;P24822 written 2 times; quant_values: 18 identifier(s), 18 row(s) dropped, e.g. PXD025503:20200716_Q2_UC_ColID_938_ProjID_2165_Trifunovic_1:label_free:protein_group:PXD025503:F8VPQ6;P24822:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
104 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
104 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 | 521,289 |
| Peptidoforms at 1% FDR | 67,071 |
| Protein groups at 1% FDR | 4,656 |
| PTM sites | 34,371 |
| Quantitative values | 388,208 |
| PSMs, all (including decoys and sub-threshold) | 827,582 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 76.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.4% |
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
- 9 / 9
- 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 | 10,357 |
| Oxidation on M | UNIMOD:35 | 6,006 |
| Deamidation on Q | UNIMOD:7 | 3,884 |
| Deamidation on N | UNIMOD:7 | 3,481 |
| Citrullination on R | UNIMOD:7 | 1,121 |
| Hydroxylation on P | UNIMOD:35 | 935 |
| Ammonia loss on N | UNIMOD:385 | 515 |
| Hydroxylation on K | UNIMOD:35 | 453 |
| Hydroxylation on N | UNIMOD:35 | 411 |
| Methylation on K | UNIMOD:34 | 408 |
| Carbamyl on X | UNIMOD:5 | 381 |
| Sodium on E | UNIMOD:30 | 332 |
| Magnesium on E | UNIMOD:956 | 301 |
| Sodium on D | UNIMOD:30 | 288 |
| Ammonia loss on C | UNIMOD:385 | 285 |
| Magnesium on D | UNIMOD:956 | 265 |
| N-acetylalanine on A | UNIMOD:1 | 245 |
| Acetylation on X | UNIMOD:1 | 200 |
| Methylation on R | UNIMOD:34 | 190 |
| Dimethylation on K | UNIMOD:36 | 186 |
| Phosphoserine on S | UNIMOD:21 | 172 |
| Formylation on K | UNIMOD:122 | 167 |
| Calcium on D | UNIMOD:951 | 148 |
| Calcium on E | UNIMOD:951 | 144 |
| Acetylation on K | UNIMOD:1 | 132 |
| Trimethylation on K | UNIMOD:37 | 123 |
| Water Loss on E | UNIMOD:27 | 121 |
| Butyrylation on K | UNIMOD:1289 | 111 |
| N-acetylmethionine on M | UNIMOD:1 | 100 |
| Carbamyl on K | UNIMOD:5 | 96 |
| Hydroxybutyrylation on K | — | 91 |
| Potassium on D | UNIMOD:530 | 89 |
| Carboxylation on E | UNIMOD:299 | 88 |
| N-acetylserine on S | UNIMOD:1 | 88 |
| Carboxylation on D | UNIMOD:299 | 83 |
| Potassium on E | UNIMOD:530 | 82 |
| Crotonylation on K | UNIMOD:1363 | 78 |
| Dimethylation on R | UNIMOD:36 | 77 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 74 |
| Succinylation on K | UNIMOD:64 | 74 |
| Nitrosylation on Y | UNIMOD:354 | 72 |
| Phosphorylation on T | UNIMOD:21 | 72 |
| Glutarylation on K | UNIMOD:1848 | 63 |
| HexNAc on T | UNIMOD:43 | 62 |
| Phosphorylation on S | UNIMOD:21 | 62 |
| HexNAc on S | UNIMOD:43 | 61 |
| Carboxylation on K | UNIMOD:299 | 60 |
| N6-acetyllysine on K | UNIMOD:1 | 59 |
| Carbamyl on M | UNIMOD:5 | 51 |
| Fe[II] on D | UNIMOD:952 | 51 |
| Malonylation on K | UNIMOD:747 | 49 |
| Fe[III] on D | UNIMOD:1870 | 48 |
| Carbamyl on C | UNIMOD:5 | 46 |
| Fe[III] on E | UNIMOD:1870 | 43 |
| Nitrosylation on C | UNIMOD:275 | 40 |
| Fe[II] on E | UNIMOD:952 | 39 |
| Phosphothreonine on T | UNIMOD:21 | 38 |
| Carbamyl on R | UNIMOD:5 | 34 |
| Pyridoxal phosphate on K | UNIMOD:46 | 33 |
| N-acetylthreonine on T | UNIMOD:1 | 30 |
| N6-succinyllysine on K | — | 28 |
| Cu[I] on D | UNIMOD:531 | 21 |
| Cu[I] on E | UNIMOD:531 | 21 |
| Phosphorylation on Y | UNIMOD:21 | 20 |
| Sulfonation on Y | UNIMOD:40 | 20 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| ADP-ribosylation on S | UNIMOD:213 | 15 |
| N6-methyllysine on K | UNIMOD:34 | 13 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 12 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 12 |
| N6-glutaryllysine on K | — | 12 |
| 4-hydroxyproline on P | UNIMOD:35 | 11 |
| Deamidated asparagine on N | UNIMOD:7 | 10 |
| N-myristoyl glycine on G | UNIMOD:45 | 10 |
| Omega-N-methylarginine on R | UNIMOD:34 | 10 |
| Glu to PyroGlu on Q | UNIMOD:28 | 8 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-malonyllysine on K | — | 4 |
| Pros-methylhistidine on H | UNIMOD:34 | 4 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| N6-crotonyllysine on K | — | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| Zinc on E | UNIMOD:954 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Hypusine on K | UNIMOD:379 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-methacryllysine on K | — | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
01c429bb8f7e8575, written 2026-10-29T10:26:33+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