Generated summary
PXD014416 is a DDA label-free dataset (Mus musculus) with 47 runs, 47 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 594,741 PSMs, 42,076 peptidoforms and 4,960 protein groups, and the repository holds 26,873 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 42076 where the producer reported 42075 (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 42076 where the producer reported 42075 (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 594741 where the producer reported 595046 (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 594741 where the producer reported 595046 (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.
high_contamination warning
19.31% of protein intensity in the worst file, 5.36% median across 47 files (DEF-QC-9 v3.5)
19.31% of protein intensity in the worst file, 5.36% median across 47 files (DEF-QC-9 v3.5)
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 105078 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3239 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 105078 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 3239 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: 7859 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: 7859 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: 1 identifier(s), 1 row(s) dropped, e.g. PXD014416:A0A087WR13;A0A571BD48 written 2 times; quant_values: 47 identifier(s), 47 row(s) dropped, e.g. PXD014416:Week0-1:label_free:protein_group:PXD014416:A0A087WR13;A0A571BD48: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: 1 identifier(s), 1 row(s) dropped, e.g. PXD014416:A0A087WR13;A0A571BD48 written 2 times; quant_values: 47 identifier(s), 47 row(s) dropped, e.g. PXD014416:Week0-1:label_free:protein_group:PXD014416:A0A087WR13;A0A571BD48:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
106 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
106 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 | 594,741 |
| Peptidoforms at 1% FDR | 42,076 |
| Protein groups at 1% FDR | 4,960 |
| PTM sites | 26,873 |
| Quantitative values | 720,151 |
| PSMs, all (including decoys and sub-threshold) | 1,292,686 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 33.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.0% |
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
- 47 / 47
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2b4533e54e28
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 9,559 |
| Oxidation on M | UNIMOD:35 | 3,575 |
| Deamidation on N | UNIMOD:7 | 2,564 |
| Deamidation on Q | UNIMOD:7 | 2,231 |
| Hydroxylation on P | UNIMOD:35 | 691 |
| Carbamyl on X | UNIMOD:5 | 401 |
| Citrullination on R | UNIMOD:7 | 383 |
| Ammonia loss on N | UNIMOD:385 | 363 |
| Magnesium on E | UNIMOD:956 | 356 |
| Sodium on E | UNIMOD:30 | 356 |
| Hydroxylation on N | UNIMOD:35 | 344 |
| Sodium on D | UNIMOD:30 | 309 |
| Magnesium on D | UNIMOD:956 | 307 |
| Methylation on K | UNIMOD:34 | 265 |
| Fe[II] on E | UNIMOD:952 | 240 |
| Hydroxylation on K | UNIMOD:35 | 230 |
| Fe[II] on D | UNIMOD:952 | 209 |
| Calcium on E | UNIMOD:951 | 195 |
| Calcium on D | UNIMOD:951 | 192 |
| Ammonia loss on C | UNIMOD:385 | 178 |
| Fe[III] on E | UNIMOD:1870 | 155 |
| Fe[III] on D | UNIMOD:1870 | 145 |
| Phosphoserine on S | UNIMOD:21 | 142 |
| Methylation on R | UNIMOD:34 | 139 |
| Carboxylation on E | UNIMOD:299 | 137 |
| N-acetylalanine on A | UNIMOD:1 | 129 |
| Carbamyl on K | UNIMOD:5 | 128 |
| Potassium on D | UNIMOD:530 | 120 |
| Acetylation on K | UNIMOD:1 | 115 |
| Water Loss on E | UNIMOD:27 | 114 |
| Potassium on E | UNIMOD:530 | 108 |
| Acetylation on X | UNIMOD:1 | 100 |
| Carbamyl on M | UNIMOD:5 | 96 |
| Phosphorylation on S | UNIMOD:21 | 95 |
| HexNAc on T | UNIMOD:43 | 90 |
| HexNAc on S | UNIMOD:43 | 87 |
| Dimethylation on K | UNIMOD:36 | 85 |
| Carboxylation on D | UNIMOD:299 | 76 |
| Formylation on K | UNIMOD:122 | 76 |
| N6-acetyllysine on K | UNIMOD:1 | 70 |
| Phosphorylation on T | UNIMOD:21 | 65 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 60 |
| 4-hydroxyproline on P | UNIMOD:35 | 58 |
| Carbamyl on R | UNIMOD:5 | 57 |
| N-acetylmethionine on M | UNIMOD:1 | 54 |
| Glutarylation on K | UNIMOD:1848 | 53 |
| N-acetylserine on S | UNIMOD:1 | 53 |
| Butyrylation on K | UNIMOD:1289 | 52 |
| Crotonylation on K | UNIMOD:1363 | 50 |
| Trimethylation on K | UNIMOD:37 | 50 |
| Carboxylation on K | UNIMOD:299 | 49 |
| Nitrosylation on Y | UNIMOD:354 | 49 |
| Dimethylation on R | UNIMOD:36 | 38 |
| Malonylation on K | UNIMOD:747 | 37 |
| Hydroxybutyrylation on K | — | 33 |
| Carbamyl on C | UNIMOD:5 | 32 |
| N6-methyllysine on K | UNIMOD:34 | 30 |
| HexNAc on Nxt | UNIMOD:43 | 28 |
| Succinylation on K | UNIMOD:64 | 27 |
| HexNAc on Nxs | UNIMOD:43 | 21 |
| Pyridoxal phosphate on K | UNIMOD:46 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 20 |
| Phosphorylation on Y | UNIMOD:21 | 20 |
| Nitrosylation on C | UNIMOD:275 | 18 |
| Omega-N-methylarginine on R | UNIMOD:34 | 18 |
| Phosphothreonine on T | UNIMOD:21 | 18 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 17 |
| Sulfonation on Y | UNIMOD:40 | 15 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 11 |
| Deamidated asparagine on N | UNIMOD:7 | 9 |
| Glu to PyroGlu on Q | UNIMOD:28 | 8 |
| N6-succinyllysine on K | — | 8 |
| N-acetylvaline on V | UNIMOD:1 | 7 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| Citrulline on R | UNIMOD:7 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| N6-methacryllysine on K | — | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-glutamyl serotonin on Q | — | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-glutaryllysine on K | — | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 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
60f78102d6f4c207, written 2026-10-29T09:33:14+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