Generated summary
PXD026335 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 940,017 PSMs, 63,382 peptidoforms and 3,805 protein groups, and the repository holds 51,105 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 940017 where the producer reported 940544 (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 940017 where the producer reported 940544 (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
14.47 avg cores of 32 allowed (S5)
14.47 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 208028 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10 duplicate entry for one site and run (identical values; same protein group); 8935 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 208028 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 10 duplicate entry for one site and run (identical values; same protein group); 8935 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: 5745 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: 5745 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), 3 row(s) dropped, e.g. PXD026335:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6 written 3 times; quant_values: 40 identifier(s), 60 row(s) dropped, e.g. PXD026335:17092_q10505_mmp_mouse_heartSS31_trypsin_LFQ_1039-5:label_free:protein_group:PXD026335:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 3 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), 3 row(s) dropped, e.g. PXD026335:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6 written 3 times; quant_values: 40 identifier(s), 60 row(s) dropped, e.g. PXD026335:17092_q10505_mmp_mouse_heartSS31_trypsin_LFQ_1039-5:label_free:protein_group:PXD026335:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KE99;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
212 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
212 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 | 940,017 |
| Peptidoforms at 1% FDR | 63,382 |
| Protein groups at 1% FDR | 3,805 |
| PTM sites | 51,105 |
| Quantitative values | 839,130 |
| PSMs, all (including decoys and sub-threshold) | 1,712,385 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 76.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
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
- b8b36ebf6016
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,270 |
| Carbamyl on X | UNIMOD:5 | 7,995 |
| Deamidation on Q | UNIMOD:7 | 4,754 |
| Deamidation on N | UNIMOD:7 | 4,440 |
| Oxidation on M | UNIMOD:35 | 3,468 |
| Carbamyl on K | UNIMOD:5 | 1,407 |
| Citrullination on R | UNIMOD:7 | 1,379 |
| Hydroxylation on P | UNIMOD:35 | 1,339 |
| Ammonia loss on N | UNIMOD:385 | 872 |
| Acetylation on K | UNIMOD:1 | 731 |
| Hydroxylation on N | UNIMOD:35 | 730 |
| Carboxylation on E | UNIMOD:299 | 644 |
| Carbamyl on M | UNIMOD:5 | 599 |
| Sodium on E | UNIMOD:30 | 599 |
| Methylation on K | UNIMOD:34 | 551 |
| Magnesium on E | UNIMOD:956 | 521 |
| Sodium on D | UNIMOD:30 | 518 |
| Hydroxylation on K | UNIMOD:35 | 496 |
| Dimethylation on K | UNIMOD:36 | 460 |
| Carboxylation on D | UNIMOD:299 | 438 |
| Magnesium on D | UNIMOD:956 | 438 |
| Phosphoserine on S | UNIMOD:21 | 421 |
| Carbamyl on R | UNIMOD:5 | 347 |
| Ammonia loss on C | UNIMOD:385 | 321 |
| Trimethylation on K | UNIMOD:37 | 311 |
| Formylation on K | UNIMOD:122 | 307 |
| Carboxylation on K | UNIMOD:299 | 258 |
| Water Loss on E | UNIMOD:27 | 255 |
| N6-acetyllysine on K | UNIMOD:1 | 254 |
| Methylation on R | UNIMOD:34 | 251 |
| Calcium on E | UNIMOD:951 | 249 |
| Carbamyl on C | UNIMOD:5 | 244 |
| Nitrosylation on Y | UNIMOD:354 | 239 |
| N-acetylalanine on A | UNIMOD:1 | 227 |
| Phosphorylation on S | UNIMOD:21 | 212 |
| Dimethylation on R | UNIMOD:36 | 200 |
| Acetylation on X | UNIMOD:1 | 194 |
| Calcium on D | UNIMOD:951 | 179 |
| Hydroxybutyrylation on K | — | 127 |
| Potassium on E | UNIMOD:530 | 126 |
| Phosphorylation on T | UNIMOD:21 | 115 |
| Succinylation on K | UNIMOD:64 | 106 |
| Crotonylation on K | UNIMOD:1363 | 98 |
| Phosphothreonine on T | UNIMOD:21 | 98 |
| N-acetylmethionine on M | UNIMOD:1 | 97 |
| Malonylation on K | UNIMOD:747 | 93 |
| Potassium on D | UNIMOD:530 | 93 |
| Butyrylation on K | UNIMOD:1289 | 91 |
| N-acetylserine on S | UNIMOD:1 | 87 |
| HexNAc on S | UNIMOD:43 | 84 |
| N6-succinyllysine on K | — | 83 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 81 |
| Glutarylation on K | UNIMOD:1848 | 75 |
| Nitrosylation on C | UNIMOD:275 | 74 |
| Fe[II] on D | UNIMOD:952 | 68 |
| Fe[II] on E | UNIMOD:952 | 68 |
| HexNAc on T | UNIMOD:43 | 62 |
| 4-hydroxyproline on P | UNIMOD:35 | 59 |
| Fe[III] on D | UNIMOD:1870 | 46 |
| Fe[III] on E | UNIMOD:1870 | 43 |
| Cu[I] on D | UNIMOD:531 | 39 |
| Pyridoxal phosphate on K | UNIMOD:46 | 35 |
| Sulfonation on Y | UNIMOD:40 | 34 |
| Omega-N-methylarginine on R | UNIMOD:34 | 30 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 27 |
| Phosphorylation on Y | UNIMOD:21 | 27 |
| Cu[I] on E | UNIMOD:531 | 25 |
| N-acetylthreonine on T | UNIMOD:1 | 23 |
| N6-methyllysine on K | UNIMOD:34 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 20 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 17 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| Phosphotyrosine on Y | UNIMOD:21 | 12 |
| N-myristoyl glycine on G | UNIMOD:45 | 9 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 9 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 8 |
| Zinc on D | UNIMOD:954 | 8 |
| Glu to PyroGlu on Q | UNIMOD:28 | 7 |
| Zinc on E | UNIMOD:954 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| N5-methylglutamine on Q | UNIMOD:34 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-malonyllysine on K | — | 5 |
| 3-hydroxyproline on P | UNIMOD:35 | 4 |
| ADP-ribosylation on S | UNIMOD:213 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| HexNAc on Nxs | UNIMOD:43 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Pros-methylhistidine on H | UNIMOD:34 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| N6-biotinyllysine on K | UNIMOD:3 | 3 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-lipoyllysine on K | UNIMOD:42 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-methacryllysine on K | — | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| S-(2,3-dicarboxypropyl)cysteine on C | — | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
24f3d62867f22860, written 2026-10-29T12:37:57+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