Generated summary
PXD047293 is a DDA label-free dataset (Rattus norvegicus) with 34 runs, 18 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 28,664 PSMs, 1,714 peptidoforms and 486 protein groups, and the repository holds 2,039 PTM sites for it. 8 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, 8 warnings and 3 for information
count_mismatch warning
The bundle holds 28664 where the producer reported 28656 (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 28664 where the producer reported 28656 (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
2.78% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
2.78% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
87.45% of protein intensity in the worst file, 87.45% median across 2 files (DEF-QC-9 v3.5)
87.45% of protein intensity in the worst file, 87.45% median across 2 files (DEF-QC-9 v3.5)
low_core_use warning
13.36 avg cores of 32 allowed (S5)
13.36 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 28656/414259 = 6.92% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 28656/414259 = 6.92% of MS2 identified (S3)
occupancy_not_stored warning
Of 9112 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 434 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 9112 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 434 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).
sdrf_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 50 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: 50 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.
excluded_from_search info
The deposited file 230517_Jarome3_Y1_01.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: f21737645c3bcb5f043543b1a63873cc06bfb9e6a74edf5fd8afc60788fda8ed.
The deposited file 230517_Jarome3_Y1_01.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: f21737645c3bcb5f043543b1a63873cc06bfb9e6a74edf5fd8afc60788fda8ed.
excluded_from_search info
The deposited file 230517_Jarome3_Y4_02.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 58f452c0f450990d1e4d25a080bd4da7f953e41f466c0693836f1160adb12e10.
The deposited file 230517_Jarome3_Y4_02.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 58f452c0f450990d1e4d25a080bd4da7f953e41f466c0693836f1160adb12e10.
occupancy_decoy_groups info
25 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
25 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 | 28,664 |
| Peptidoforms at 1% FDR | 1,714 |
| Protein groups at 1% FDR | 486 |
| PTM sites | 2,039 |
| Quantitative values | 52,620 |
| PSMs, all (including decoys and sub-threshold) | 156,525 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 6.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 52.6% |
How it was measured
- Organism searched
- Rattus norvegicus (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 34 / 18
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000002494_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 9df4ce025f23
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 517 |
| Nethylmaleimide on C | UNIMOD:108 | 66 |
| Hydroxylation on P | UNIMOD:35 | 53 |
| Deamidation on N | UNIMOD:7 | 48 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 35 |
| Hydroxylation on N | UNIMOD:35 | 31 |
| Ammonia loss on N | UNIMOD:385 | 25 |
| Deamidation on Q | UNIMOD:7 | 25 |
| N-acetylalanine on A | UNIMOD:1 | 16 |
| Acetylation on X | UNIMOD:1 | 13 |
| Phosphoserine on S | UNIMOD:21 | 12 |
| Water Loss on E | UNIMOD:27 | 12 |
| Dimethylation on K | UNIMOD:36 | 9 |
| Acetylation on K | UNIMOD:1 | 8 |
| Citrullination on R | UNIMOD:7 | 8 |
| Hydroxylation on K | UNIMOD:35 | 8 |
| Formylation on K | UNIMOD:122 | 7 |
| 4-hydroxyproline on P | UNIMOD:35 | 6 |
| Dimethylation on R | UNIMOD:36 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 5 |
| Methylation on R | UNIMOD:34 | 4 |
| N-acetylmethionine on M | UNIMOD:1 | 4 |
| N-acetylserine on S | UNIMOD:1 | 4 |
| Phosphorylation on S | UNIMOD:21 | 4 |
| Phosphothreonine on T | UNIMOD:21 | 4 |
| Carboxylation on E | UNIMOD:299 | 3 |
| Deamidated asparagine on N | UNIMOD:7 | 3 |
| N-acetylthreonine on T | UNIMOD:1 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Fe[II] on E | UNIMOD:952 | 2 |
| Methylation on K | UNIMOD:34 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N6-acetyllysine on K | UNIMOD:1 | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| Ammonia loss on C | UNIMOD:385 | 1 |
| Calcium on E | UNIMOD:951 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Carbamyl on K | UNIMOD:5 | 1 |
| Carbamyl on R | UNIMOD:5 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Fe[II] on D | UNIMOD:952 | 1 |
| Glutarylation on K | UNIMOD:1848 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| Phosphorylation on T | UNIMOD:21 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-methylhistidine on H | UNIMOD:34 | 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
bcd862892400a6d0, written 2026-10-29T09:42:53+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