Generated summary
PXD014097 is a DDA label-free dataset (Mus musculus) with 12 runs, 12 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 150,342 PSMs, 20,939 peptidoforms and 4,072 protein groups, and the repository holds 19,650 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 1 for information
count_mismatch warning
The bundle holds 150342 where the producer reported 150373 (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 150342 where the producer reported 150373 (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.
cysteine_poor warning
3.14% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
3.14% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
low_core_use warning
14.79 avg cores of 32 allowed (S5)
14.79 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 141919 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2985 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 141919 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2985 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: 128 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: 128 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.
occupancy_decoy_groups info
169 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
169 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 | 150,342 |
| Peptidoforms at 1% FDR | 20,939 |
| Protein groups at 1% FDR | 4,072 |
| PTM sites | 19,650 |
| Quantitative values | 255,529 |
| PSMs, all (including decoys and sub-threshold) | 210,248 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 52.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 7.0% |
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
- phospho
- Instrument vendor
- not recorded
- Runs / samples
- 12 / 12
- 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 |
|---|---|---|
| Phosphoserine on S | UNIMOD:21 | 5,758 |
| Phosphorylation on S | UNIMOD:21 | 5,020 |
| Oxidation on M | UNIMOD:35 | 2,620 |
| Phosphorylation on T | UNIMOD:21 | 1,481 |
| Carbamidomethyl on C | UNIMOD:4 | 750 |
| Phosphothreonine on T | UNIMOD:21 | 638 |
| Deamidation on N | UNIMOD:7 | 412 |
| Phosphorylation on Y | UNIMOD:21 | 307 |
| Hydroxylation on P | UNIMOD:35 | 282 |
| Deamidation on Q | UNIMOD:7 | 240 |
| Sulfonation on Y | UNIMOD:40 | 170 |
| Sodium on E | UNIMOD:30 | 120 |
| Magnesium on E | UNIMOD:956 | 115 |
| N-acetylalanine on A | UNIMOD:1 | 114 |
| Phosphotyrosine on Y | UNIMOD:21 | 114 |
| Sodium on D | UNIMOD:30 | 105 |
| Hydroxylation on N | UNIMOD:35 | 91 |
| Magnesium on D | UNIMOD:956 | 77 |
| Ammonia loss on N | UNIMOD:385 | 73 |
| N-acetylserine on S | UNIMOD:1 | 73 |
| Citrullination on R | UNIMOD:7 | 68 |
| Acetylation on X | UNIMOD:1 | 67 |
| Hydroxylation on K | UNIMOD:35 | 67 |
| Calcium on E | UNIMOD:951 | 45 |
| Calcium on D | UNIMOD:951 | 40 |
| Formylation on K | UNIMOD:122 | 38 |
| Methylation on K | UNIMOD:34 | 37 |
| Water Loss on E | UNIMOD:27 | 35 |
| Carbamyl on X | UNIMOD:5 | 32 |
| N-acetylmethionine on M | UNIMOD:1 | 32 |
| Pyridoxal phosphate on K | UNIMOD:46 | 31 |
| HexNAc on S | UNIMOD:43 | 20 |
| Potassium on E | UNIMOD:530 | 19 |
| Ammonia loss on C | UNIMOD:385 | 18 |
| Methylation on R | UNIMOD:34 | 18 |
| Acetylation on K | UNIMOD:1 | 16 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| N6-methyllysine on K | UNIMOD:34 | 13 |
| N6-acetyllysine on K | UNIMOD:1 | 11 |
| Potassium on D | UNIMOD:530 | 11 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 10 |
| Carboxylation on E | UNIMOD:299 | 9 |
| Cu[I] on D | UNIMOD:531 | 7 |
| Dimethylation on K | UNIMOD:36 | 7 |
| Dimethylation on R | UNIMOD:36 | 7 |
| Glutarylation on K | UNIMOD:1848 | 7 |
| HexNAc on T | UNIMOD:43 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| N-acetylthreonine on T | UNIMOD:1 | 7 |
| 4-hydroxyproline on P | UNIMOD:35 | 6 |
| N-myristoyl glycine on G | UNIMOD:45 | 6 |
| Carboxylation on D | UNIMOD:299 | 5 |
| Malonylation on K | UNIMOD:747 | 5 |
| Cu[I] on E | UNIMOD:531 | 4 |
| Hydroxybutyrylation on K | — | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carbamyl on K | UNIMOD:5 | 3 |
| Carbamyl on M | UNIMOD:5 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| Omega-N-methylarginine on R | UNIMOD:34 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-succinyllysine on K | — | 1 |
| Nitrosylation on Y | UNIMOD:354 | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
7c77b72428450704, written 2026-10-29T09:29:37+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