Generated summary
PXD011314 is a DDA label-free dataset (Homo sapiens) with 17 runs, 17 samples and enrichment: chemical_probe. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 4,868 PSMs, 391 peptidoforms and 57 protein groups, and the repository holds 580 PTM sites for it. 7 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, 7 warnings and 1 for information
calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)
GPTMD/search ran on uncalibrated spectra (S7)
high_contamination warning
54.83% of protein intensity in the worst file, 25.70% median across 17 files (DEF-QC-9 v3.5)
54.83% of protein intensity in the worst file, 25.70% median across 17 files (DEF-QC-9 v3.5)
low_core_use warning
15.55 avg cores of 32 allowed (S5)
15.55 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: 4868/552408 = 0.88% 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: 4868/552408 = 0.88% of MS2 identified (S3)
occupancy_not_stored warning
Of 1491 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12 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 1491 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12 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_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: Blood. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: Blood. Match on it as text; it has not been mapped to a term.
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: 29 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: 29 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
5 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
5 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 | 4,868 |
| Peptidoforms at 1% FDR | 391 |
| Protein groups at 1% FDR | 57 |
| PTM sites | 580 |
| Quantitative values | 3,949 |
| PSMs, all (including decoys and sub-threshold) | 87,671 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 0.9% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 7.1% |
How it was measured
- Organism searched
- Homo sapiens (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- chemical_probe
- Instrument vendor
- Thermo
- Runs / samples
- 17 / 17
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 53 |
| Carbamidomethyl on C | UNIMOD:4 | 38 |
| Carbamyl on X | UNIMOD:5 | 31 |
| Calcium on E | UNIMOD:951 | 27 |
| Methylation on K | UNIMOD:34 | 21 |
| Hydroxylation on P | UNIMOD:35 | 17 |
| Magnesium on E | UNIMOD:956 | 17 |
| Deamidation on N | UNIMOD:7 | 15 |
| HexNAc on T | UNIMOD:43 | 11 |
| Phosphorylation on T | UNIMOD:21 | 11 |
| Deamidation on Q | UNIMOD:7 | 10 |
| HexNAc on S | UNIMOD:43 | 10 |
| Hydroxylation on K | UNIMOD:35 | 9 |
| Phosphorylation on S | UNIMOD:21 | 9 |
| Potassium on E | UNIMOD:530 | 9 |
| Sodium on E | UNIMOD:30 | 9 |
| Carboxylation on E | UNIMOD:299 | 8 |
| Citrullination on R | UNIMOD:7 | 8 |
| Fe[III] on E | UNIMOD:1870 | 8 |
| Fe[II] on E | UNIMOD:952 | 8 |
| Carbamyl on K | UNIMOD:5 | 7 |
| Fe[III] on D | UNIMOD:1870 | 7 |
| Hydroxybutyrylation on K | — | 7 |
| Sulfonation on Y | UNIMOD:40 | 7 |
| Ammonia loss on N | UNIMOD:385 | 6 |
| Calcium on D | UNIMOD:951 | 6 |
| Crotonylation on K | UNIMOD:1363 | 6 |
| Fe[II] on D | UNIMOD:952 | 6 |
| Formylation on K | UNIMOD:122 | 6 |
| Hydroxylation on N | UNIMOD:35 | 6 |
| ADP-ribosylation on S | UNIMOD:213 | 5 |
| Acetylation on K | UNIMOD:1 | 5 |
| Carbamyl on C | UNIMOD:5 | 5 |
| Cu[I] on E | UNIMOD:531 | 5 |
| Dimethylation on K | UNIMOD:36 | 5 |
| Magnesium on D | UNIMOD:956 | 5 |
| Methylation on R | UNIMOD:34 | 5 |
| Nitrosylation on C | UNIMOD:275 | 5 |
| Phosphorylation on Y | UNIMOD:21 | 5 |
| Butyrylation on K | UNIMOD:1289 | 4 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 4 |
| Glutarylation on K | UNIMOD:1848 | 4 |
| Potassium on D | UNIMOD:530 | 4 |
| Sodium on D | UNIMOD:30 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| Trimethylation on K | UNIMOD:37 | 4 |
| Carbamyl on R | UNIMOD:5 | 3 |
| Dimethylation on R | UNIMOD:36 | 3 |
| Malonylation on K | UNIMOD:747 | 3 |
| Phosphoserine on S | UNIMOD:21 | 3 |
| Pyridoxal phosphate on K | UNIMOD:46 | 3 |
| Carboxylation on D | UNIMOD:299 | 2 |
| Cu[I] on D | UNIMOD:531 | 2 |
| Nitrosylation on Y | UNIMOD:354 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| Acetylation on X | UNIMOD:1 | 1 |
| Carboxylation on K | UNIMOD:299 | 1 |
| N-acetylalanine on A | UNIMOD:1 | 1 |
| N6-succinyllysine on K | — | 1 |
| Phosphothreonine on T | UNIMOD:21 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Sulfocysteine on C | UNIMOD:40 | 1 |
| Water Loss on E | UNIMOD:27 | 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
227665124db6f3b5, written 2026-10-29T09:51:06+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group