Generated summary
PXD035107 is a DDA label-free dataset (Mus musculus) with 8 runs, 8 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 69,974 PSMs, 12,490 peptidoforms and 1,442 protein groups, and the repository holds 11,612 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 69974 where the producer reported 70041 (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 69974 where the producer reported 70041 (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
4.16% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
4.16% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
low_core_use warning
11.9 avg cores of 32 allowed (S5)
11.9 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 64622 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 826 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 64622 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 826 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: 638 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: 638 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
131 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
131 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 | 69,974 |
| Peptidoforms at 1% FDR | 12,490 |
| Protein groups at 1% FDR | 1,442 |
| PTM sites | 11,612 |
| Quantitative values | 80,820 |
| PSMs, all (including decoys and sub-threshold) | 85,157 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 44.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.2% |
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
- 8 / 8
- 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 |
|---|---|---|
| Phosphorylation on S | UNIMOD:21 | 3,011 |
| Phosphoserine on S | UNIMOD:21 | 1,826 |
| Phosphorylation on T | UNIMOD:21 | 1,363 |
| Carbamyl on X | UNIMOD:5 | 944 |
| Carbamidomethyl on C | UNIMOD:4 | 538 |
| Oxidation on M | UNIMOD:35 | 435 |
| Phosphorylation on Y | UNIMOD:21 | 408 |
| Deamidation on N | UNIMOD:7 | 323 |
| Sodium on E | UNIMOD:30 | 316 |
| Calcium on E | UNIMOD:951 | 275 |
| Phosphothreonine on T | UNIMOD:21 | 269 |
| Deamidation on Q | UNIMOD:7 | 191 |
| Sodium on D | UNIMOD:30 | 174 |
| Hydroxylation on P | UNIMOD:35 | 169 |
| Calcium on D | UNIMOD:951 | 161 |
| Sulfonation on Y | UNIMOD:40 | 141 |
| Ammonia loss on N | UNIMOD:385 | 71 |
| Carbamyl on K | UNIMOD:5 | 60 |
| Phosphotyrosine on Y | UNIMOD:21 | 53 |
| Water Loss on E | UNIMOD:27 | 52 |
| ADP-ribosylation on S | UNIMOD:213 | 48 |
| Potassium on D | UNIMOD:530 | 45 |
| Acetylation on X | UNIMOD:1 | 41 |
| 4-hydroxyproline on P | UNIMOD:35 | 40 |
| N-acetylalanine on A | UNIMOD:1 | 39 |
| Ammonia loss on C | UNIMOD:385 | 35 |
| HexNAc on T | UNIMOD:43 | 35 |
| Magnesium on E | UNIMOD:956 | 34 |
| Potassium on E | UNIMOD:530 | 34 |
| HexNAc on S | UNIMOD:43 | 29 |
| Hydroxylation on K | UNIMOD:35 | 29 |
| N-acetylserine on S | UNIMOD:1 | 26 |
| Fe[III] on E | UNIMOD:1870 | 25 |
| Carbamyl on R | UNIMOD:5 | 24 |
| Magnesium on D | UNIMOD:956 | 24 |
| Citrullination on R | UNIMOD:7 | 21 |
| Fe[III] on D | UNIMOD:1870 | 20 |
| Hydroxylation on N | UNIMOD:35 | 18 |
| Carboxylation on E | UNIMOD:299 | 14 |
| Nitrosylation on Y | UNIMOD:354 | 14 |
| Carbamyl on M | UNIMOD:5 | 13 |
| Carboxylation on D | UNIMOD:299 | 12 |
| Acetylation on K | UNIMOD:1 | 11 |
| Cu[I] on E | UNIMOD:531 | 10 |
| N-acetylmethionine on M | UNIMOD:1 | 10 |
| N6-acetyllysine on K | UNIMOD:1 | 9 |
| Methylation on K | UNIMOD:34 | 8 |
| Cu[I] on D | UNIMOD:531 | 7 |
| Fe[II] on D | UNIMOD:952 | 7 |
| Methylation on R | UNIMOD:34 | 7 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| N-acetylthreonine on T | UNIMOD:1 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 6 |
| Zinc on E | UNIMOD:954 | 6 |
| Carboxylation on K | UNIMOD:299 | 5 |
| Fe[II] on E | UNIMOD:952 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 5 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 4 |
| Dimethylation on R | UNIMOD:36 | 4 |
| Glutarylation on K | UNIMOD:1848 | 4 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 4 |
| Pyridoxal phosphate on K | UNIMOD:46 | 4 |
| Dimethylation on K | UNIMOD:36 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 3 |
| Trimethylation on K | UNIMOD:37 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Formylation on K | UNIMOD:122 | 2 |
| Malonylation on K | UNIMOD:747 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-succinyllysine on K | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
c882c9b253d4b1bb, written 2026-10-29T09:47:55+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