Generated summary
PXD010115 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 119,030 PSMs, 10,258 peptidoforms and 445 protein groups, and the repository holds 7,952 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
count_mismatch warning
The bundle holds 10258 where the producer reported 10257 (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 10258 where the producer reported 10257 (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 119030 where the producer reported 119048 (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 119030 where the producer reported 119048 (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
6.99% of protein intensity in the worst file, 3.14% median across 12 files (DEF-QC-9 v3.5)
6.99% of protein intensity in the worst file, 3.14% median across 12 files (DEF-QC-9 v3.5)
low_core_use warning
14.78 avg cores of 32 allowed (S5)
14.78 avg cores of 32 allowed (S5)
occupancy_not_stored warning
Of 19129 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6 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 19129 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6 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 serum. 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 serum. 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: 651 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: 651 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
68 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
68 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 | 119,030 |
| Peptidoforms at 1% FDR | 10,258 |
| Protein groups at 1% FDR | 445 |
| PTM sites | 7,952 |
| Quantitative values | 72,116 |
| PSMs, all (including decoys and sub-threshold) | 192,315 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 54.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.5% |
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
- none
- Instrument vendor
- Thermo
- Runs / samples
- 12 / 12
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 2,607 |
| Deamidation on N | UNIMOD:7 | 1,059 |
| Oxidation on M | UNIMOD:35 | 838 |
| Deamidation on Q | UNIMOD:7 | 819 |
| Hydroxylation on P | UNIMOD:35 | 373 |
| Citrullination on R | UNIMOD:7 | 223 |
| Ammonia loss on N | UNIMOD:385 | 216 |
| Hydroxylation on N | UNIMOD:35 | 180 |
| Ammonia loss on C | UNIMOD:385 | 130 |
| Hydroxylation on K | UNIMOD:35 | 115 |
| Methylation on K | UNIMOD:34 | 88 |
| Methylation on R | UNIMOD:34 | 64 |
| Fe[III] on E | UNIMOD:1870 | 59 |
| Phosphoserine on S | UNIMOD:21 | 59 |
| Fe[II] on E | UNIMOD:952 | 48 |
| Fe[III] on D | UNIMOD:1870 | 47 |
| Water Loss on E | UNIMOD:27 | 45 |
| Magnesium on E | UNIMOD:956 | 44 |
| Trimethylation on K | UNIMOD:37 | 42 |
| Dimethylation on K | UNIMOD:36 | 40 |
| Acetylation on K | UNIMOD:1 | 39 |
| Magnesium on D | UNIMOD:956 | 37 |
| Fe[II] on D | UNIMOD:952 | 35 |
| Sodium on D | UNIMOD:30 | 33 |
| Sodium on E | UNIMOD:30 | 30 |
| Formylation on K | UNIMOD:122 | 29 |
| Phosphorylation on S | UNIMOD:21 | 27 |
| Dimethylation on R | UNIMOD:36 | 26 |
| Phosphorylation on T | UNIMOD:21 | 24 |
| Calcium on D | UNIMOD:951 | 17 |
| Calcium on E | UNIMOD:951 | 15 |
| Carbamyl on M | UNIMOD:5 | 15 |
| Carboxylation on E | UNIMOD:299 | 15 |
| Carbamyl on X | UNIMOD:5 | 13 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 13 |
| Glutarylation on K | UNIMOD:1848 | 13 |
| Potassium on D | UNIMOD:530 | 12 |
| Potassium on E | UNIMOD:530 | 12 |
| Sulfonation on Y | UNIMOD:40 | 12 |
| 4-hydroxyproline on P | UNIMOD:35 | 11 |
| Carbamyl on K | UNIMOD:5 | 11 |
| Phosphothreonine on T | UNIMOD:21 | 11 |
| Butyrylation on K | UNIMOD:1289 | 10 |
| HexNAc on T | UNIMOD:43 | 10 |
| Nitrosylation on C | UNIMOD:275 | 10 |
| Carbamyl on C | UNIMOD:5 | 9 |
| HexNAc on S | UNIMOD:43 | 9 |
| N6-acetyllysine on K | UNIMOD:1 | 9 |
| Sulfotyrosine on Y | UNIMOD:40 | 8 |
| Phosphorylation on Y | UNIMOD:21 | 6 |
| Succinylation on K | UNIMOD:64 | 6 |
| Carboxylation on D | UNIMOD:299 | 5 |
| Carboxylation on K | UNIMOD:299 | 5 |
| Hydroxyproline on P | UNIMOD:35 | 5 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| (3R)-3-hydroxyaspartate on D | UNIMOD:35 | 3 |
| N-acetylalanine on A | UNIMOD:1 | 3 |
| N6-succinyllysine on K | — | 3 |
| Nitrosylation on Y | UNIMOD:354 | 3 |
| Omega-N-methylarginine on R | UNIMOD:34 | 3 |
| Acetylation on X | UNIMOD:1 | 2 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Deamidated asparagine on N | UNIMOD:7 | 2 |
| Malonylation on K | UNIMOD:747 | 2 |
| (3R)-3-hydroxyasparagine on N | UNIMOD:35 | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| N-acetylmethionine on M | UNIMOD:1 | 1 |
| N-acetylserine on S | UNIMOD:1 | 1 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 1 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 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
d6d3770b0aa808c2, written 2026-10-29T09:36:42+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