Generated summary
PXD041376 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 1,665,643 PSMs, 57,845 peptidoforms and 6,181 protein groups, and the repository holds 25,872 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 57846 where the producer reported 57841 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 57846 where the producer reported 57841 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
count_mismatch warning
The bundle holds 1.66564e+06 where the producer reported 1.66566e+06 (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 1.66564e+06 where the producer reported 1.66566e+06 (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.
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 122204 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11671 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 122204 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11671 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: 4520 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: 4520 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), 6 row(s) dropped, e.g. PXD041376:A0A1L1SQT2;A2AV41;L7MTT1;Q7TR35;Q7TR49 written 5 times; quant_values: 40 identifier(s), 120 row(s) dropped, e.g. PXD041376:20221230_DS_Col99E_emma_BaF_R1_7:label_free:protein_group:PXD041376:A0A1L1SQT2;A2AV41;L7MTT1;Q7TR35;Q7TR49:QuantProject:DEF-PROT-SPC written 5 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), 6 row(s) dropped, e.g. PXD041376:A0A1L1SQT2;A2AV41;L7MTT1;Q7TR35;Q7TR49 written 5 times; quant_values: 40 identifier(s), 120 row(s) dropped, e.g. PXD041376:20221230_DS_Col99E_emma_BaF_R1_7:label_free:protein_group:PXD041376:A0A1L1SQT2;A2AV41;L7MTT1;Q7TR35;Q7TR49:QuantProject:DEF-PROT-SPC written 5 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
977 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
977 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 | 1,665,643 |
| Peptidoforms at 1% FDR | 57,845 |
| Protein groups at 1% FDR | 6,181 |
| PTM sites | 25,872 |
| Quantitative values | 1,051,598 |
| PSMs, all (including decoys and sub-threshold) | 3,927,648 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 76.0% |
| 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
- 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
- 0095bcefc3f5
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,487 |
| Oxidation on M | UNIMOD:35 | 2,551 |
| Deamidation on N | UNIMOD:7 | 2,191 |
| Deamidation on Q | UNIMOD:7 | 2,170 |
| Ammonia loss on N | UNIMOD:385 | 756 |
| Hydroxylation on P | UNIMOD:35 | 598 |
| Citrullination on R | UNIMOD:7 | 524 |
| Phosphoserine on S | UNIMOD:21 | 427 |
| Hydroxylation on N | UNIMOD:35 | 360 |
| Fe[III] on E | UNIMOD:1870 | 358 |
| Formylation on K | UNIMOD:122 | 308 |
| Fe[III] on D | UNIMOD:1870 | 271 |
| Sodium on E | UNIMOD:30 | 269 |
| N-acetylalanine on A | UNIMOD:1 | 246 |
| Acetylation on X | UNIMOD:1 | 219 |
| Ammonia loss on C | UNIMOD:385 | 217 |
| Sodium on D | UNIMOD:30 | 173 |
| Hydroxylation on K | UNIMOD:35 | 160 |
| N-acetylmethionine on M | UNIMOD:1 | 135 |
| Phosphorylation on S | UNIMOD:21 | 132 |
| Phosphorylation on T | UNIMOD:21 | 127 |
| Water Loss on E | UNIMOD:27 | 127 |
| Fe[II] on E | UNIMOD:952 | 111 |
| Fe[II] on D | UNIMOD:952 | 103 |
| Carbamyl on X | UNIMOD:5 | 97 |
| N6-acetyllysine on K | UNIMOD:1 | 97 |
| Phosphothreonine on T | UNIMOD:21 | 88 |
| Methylation on K | UNIMOD:34 | 84 |
| N-acetylserine on S | UNIMOD:1 | 81 |
| Magnesium on E | UNIMOD:956 | 69 |
| Calcium on E | UNIMOD:951 | 67 |
| Magnesium on D | UNIMOD:956 | 64 |
| Omega-N-methylarginine on R | UNIMOD:34 | 49 |
| Calcium on D | UNIMOD:951 | 47 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 43 |
| Acetylation on K | UNIMOD:1 | 42 |
| HexNAc on S | UNIMOD:43 | 39 |
| Dimethylation on K | UNIMOD:36 | 36 |
| HexNAc on T | UNIMOD:43 | 36 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 35 |
| Dimethylation on R | UNIMOD:36 | 34 |
| Methylation on R | UNIMOD:34 | 34 |
| Potassium on E | UNIMOD:530 | 29 |
| Crotonylation on K | UNIMOD:1363 | 21 |
| N-acetylthreonine on T | UNIMOD:1 | 20 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 18 |
| N6-glutaryllysine on K | — | 18 |
| N6-succinyllysine on K | — | 18 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 17 |
| Trimethylation on K | UNIMOD:37 | 17 |
| Carbamyl on M | UNIMOD:5 | 15 |
| Phosphorylation on Y | UNIMOD:21 | 15 |
| Potassium on D | UNIMOD:530 | 15 |
| N5-methylglutamine on Q | UNIMOD:34 | 13 |
| N6-methyllysine on K | UNIMOD:34 | 12 |
| Sulfonation on Y | UNIMOD:40 | 12 |
| Nitrosylation on C | UNIMOD:275 | 11 |
| Nitrosylation on Y | UNIMOD:354 | 11 |
| Carboxylation on D | UNIMOD:299 | 10 |
| Glutarylation on K | UNIMOD:1848 | 10 |
| Carbamyl on K | UNIMOD:5 | 9 |
| Pyridoxal phosphate on K | UNIMOD:46 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| Dimethylated arginine on R | UNIMOD:36 | 8 |
| Carboxylation on E | UNIMOD:299 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| Carbamyl on C | UNIMOD:5 | 6 |
| Carbamyl on R | UNIMOD:5 | 6 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 6 |
| 4-hydroxyproline on P | UNIMOD:35 | 5 |
| ADP-ribosylation on S | UNIMOD:213 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Glu to PyroGlu on Q | UNIMOD:28 | 1 |
| Hydroxybutyrylation on K | — | 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-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 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
e293b4f93002772b, written 2026-10-29T12:30:25+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group