Generated summary
PXD030776 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 139,095 PSMs, 14,823 peptidoforms and 2,111 protein groups, and the repository holds 7,684 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 139095 where the producer reported 139112 (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 139095 where the producer reported 139112 (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
11.38% of protein intensity in the worst file, 8.54% median across 12 files (DEF-QC-9 v3.5)
11.38% of protein intensity in the worst file, 8.54% median across 12 files (DEF-QC-9 v3.5)
low_core_use warning
14.54 avg cores of 32 allowed (S5)
14.54 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 26814 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1822 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 26814 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 1822 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: 2049 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: 2049 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
10 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
10 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 | 139,095 |
| Peptidoforms at 1% FDR | 14,823 |
| Protein groups at 1% FDR | 2,111 |
| PTM sites | 7,684 |
| Quantitative values | 139,157 |
| PSMs, all (including decoys and sub-threshold) | 223,386 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 52.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 8.7% |
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
- immunoprecipitation
- Instrument vendor
- not recorded
- Runs / samples
- 12 / 12
- Sample metadata
- absent
- 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 | 2,416 |
| Oxidation on M | UNIMOD:35 | 1,037 |
| Carbamyl on X | UNIMOD:5 | 524 |
| Deamidation on N | UNIMOD:7 | 250 |
| Fe[III] on E | UNIMOD:1870 | 218 |
| Deamidation on Q | UNIMOD:7 | 197 |
| Fe[III] on D | UNIMOD:1870 | 191 |
| Ammonia loss on N | UNIMOD:385 | 137 |
| Hydroxylation on P | UNIMOD:35 | 117 |
| Carbamyl on K | UNIMOD:5 | 107 |
| N-acetylalanine on A | UNIMOD:1 | 105 |
| Sodium on E | UNIMOD:30 | 94 |
| Citrullination on R | UNIMOD:7 | 92 |
| Ammonia loss on C | UNIMOD:385 | 91 |
| Hydroxylation on N | UNIMOD:35 | 90 |
| Calcium on D | UNIMOD:951 | 87 |
| Sodium on D | UNIMOD:30 | 87 |
| Fe[II] on D | UNIMOD:952 | 84 |
| Hydroxylation on K | UNIMOD:35 | 84 |
| Fe[II] on E | UNIMOD:952 | 74 |
| Acetylation on K | UNIMOD:1 | 61 |
| Calcium on E | UNIMOD:951 | 61 |
| Magnesium on D | UNIMOD:956 | 61 |
| Nitrosylation on Y | UNIMOD:354 | 60 |
| Magnesium on E | UNIMOD:956 | 55 |
| Carbamyl on R | UNIMOD:5 | 54 |
| Carbamyl on M | UNIMOD:5 | 50 |
| N-acetylmethionine on M | UNIMOD:1 | 50 |
| Methylation on K | UNIMOD:34 | 47 |
| Potassium on D | UNIMOD:530 | 41 |
| Cu[I] on D | UNIMOD:531 | 39 |
| N-acetylserine on S | UNIMOD:1 | 38 |
| Water Loss on E | UNIMOD:27 | 32 |
| Formylation on K | UNIMOD:122 | 29 |
| Acetylation on X | UNIMOD:1 | 28 |
| Potassium on E | UNIMOD:530 | 28 |
| Carboxylation on D | UNIMOD:299 | 26 |
| Phosphoserine on S | UNIMOD:21 | 25 |
| Methylation on R | UNIMOD:34 | 23 |
| Dimethylation on K | UNIMOD:36 | 22 |
| Butyrylation on K | UNIMOD:1289 | 17 |
| Carboxylation on E | UNIMOD:299 | 17 |
| Dimethylation on R | UNIMOD:36 | 16 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 16 |
| Phosphorylation on S | UNIMOD:21 | 14 |
| Cu[I] on E | UNIMOD:531 | 11 |
| Zinc on D | UNIMOD:954 | 11 |
| Crotonylation on K | UNIMOD:1363 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 9 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 9 |
| N6-acetyllysine on K | UNIMOD:1 | 9 |
| Phosphorylation on T | UNIMOD:21 | 9 |
| Carbamyl on C | UNIMOD:5 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| Succinylation on K | UNIMOD:64 | 8 |
| Carboxylation on K | UNIMOD:299 | 7 |
| Nitrosylation on C | UNIMOD:275 | 7 |
| Trimethylation on K | UNIMOD:37 | 7 |
| Glutarylation on K | UNIMOD:1848 | 6 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 5 |
| Phosphothreonine on T | UNIMOD:21 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Zinc on E | UNIMOD:954 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-myristoyl glycine on G | UNIMOD:45 | 4 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| Sulfonation on Y | UNIMOD:40 | 4 |
| HexNAc on T | UNIMOD:43 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| HexNAc on S | UNIMOD:43 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| Malonylation on K | UNIMOD:747 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-succinyllysine on K | — | 2 |
| Omega-N-methylarginine on R | UNIMOD:34 | 2 |
| Phosphotyrosine on Y | UNIMOD:21 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
ca8249add458b3ea, written 2026-10-29T09:34:05+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