Generated summary
PXD060982 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 327,734 PSMs, 42,460 peptidoforms and 6,060 protein groups, and the repository holds 49,503 PTM sites for it. 5 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, 5 warnings and 2 for information
count_mismatch warning
The bundle holds 327734 where the producer reported 327894 (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 327734 where the producer reported 327894 (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.
low_core_use warning
13.83 avg cores of 32 allowed (S5)
13.83 avg cores of 32 allowed (S5)
occupancy_not_stored warning
Of 244499 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 3835 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 244499 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 3835 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: Ependymal cell. 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: Ependymal cell. 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: 200 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: 200 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.
collapsed_duplicate_rows info
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD060982:O88207;O88207-2 written 2 times; quant_values: 8 identifier(s), 8 row(s) dropped, e.g. PXD060982:220208_36014_AS_L:label_free:protein_group:PXD060982:O88207;O88207-2:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
The producer wrote some rows more than once, identical in every column, and the copies were dropped so each identifier appears once. Nothing was lost: the kept row is byte-for-byte what the duplicates said. Rows that share an identifier and disagree anywhere are still refused rather than collapsed. protein_groups: 1 identifier(s), 1 row(s) dropped, e.g. PXD060982:O88207;O88207-2 written 2 times; quant_values: 8 identifier(s), 8 row(s) dropped, e.g. PXD060982:220208_36014_AS_L:label_free:protein_group:PXD060982:O88207;O88207-2:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
267 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
267 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 | 327,734 |
| Peptidoforms at 1% FDR | 42,460 |
| Protein groups at 1% FDR | 6,060 |
| PTM sites | 49,503 |
| Quantitative values | 318,185 |
| PSMs, all (including decoys and sub-threshold) | 390,816 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 38.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.7% |
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
- Thermo
- Runs / samples
- 8 / 8
- Sample metadata
- trusted
- 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 | 15,614 |
| Phosphoserine on S | UNIMOD:21 | 9,859 |
| Carbamidomethyl on C | UNIMOD:4 | 5,561 |
| Phosphorylation on T | UNIMOD:21 | 4,794 |
| Oxidation on M | UNIMOD:35 | 3,586 |
| Phosphothreonine on T | UNIMOD:21 | 1,277 |
| Phosphorylation on Y | UNIMOD:21 | 1,073 |
| Deamidation on Q | UNIMOD:7 | 1,037 |
| Hydroxylation on P | UNIMOD:35 | 727 |
| Deamidation on N | UNIMOD:7 | 706 |
| Sulfonation on Y | UNIMOD:40 | 645 |
| Calcium on E | UNIMOD:951 | 340 |
| Calcium on D | UNIMOD:951 | 321 |
| Sodium on D | UNIMOD:30 | 315 |
| Sodium on E | UNIMOD:30 | 313 |
| Hydroxylation on N | UNIMOD:35 | 233 |
| Hydroxylation on K | UNIMOD:35 | 222 |
| Citrullination on R | UNIMOD:7 | 199 |
| Ammonia loss on N | UNIMOD:385 | 189 |
| Phosphotyrosine on Y | UNIMOD:21 | 187 |
| Acetylation on X | UNIMOD:1 | 174 |
| N-acetylalanine on A | UNIMOD:1 | 143 |
| Carbamyl on X | UNIMOD:5 | 136 |
| N-acetylserine on S | UNIMOD:1 | 118 |
| Magnesium on E | UNIMOD:956 | 110 |
| Ammonia loss on C | UNIMOD:385 | 102 |
| Potassium on E | UNIMOD:530 | 97 |
| Fe[III] on E | UNIMOD:1870 | 86 |
| Magnesium on D | UNIMOD:956 | 69 |
| HexNAc on S | UNIMOD:43 | 68 |
| N-acetylmethionine on M | UNIMOD:1 | 68 |
| Potassium on D | UNIMOD:530 | 67 |
| HexNAc on T | UNIMOD:43 | 58 |
| Fe[III] on D | UNIMOD:1870 | 54 |
| Water Loss on E | UNIMOD:27 | 49 |
| Fe[II] on D | UNIMOD:952 | 48 |
| Fe[II] on E | UNIMOD:952 | 47 |
| Methylation on K | UNIMOD:34 | 46 |
| Acetylation on K | UNIMOD:1 | 41 |
| Methylation on R | UNIMOD:34 | 40 |
| Formylation on K | UNIMOD:122 | 36 |
| Succinylation on K | UNIMOD:64 | 34 |
| Cu[I] on E | UNIMOD:531 | 27 |
| Dimethylation on R | UNIMOD:36 | 25 |
| Omega-N-methylarginine on R | UNIMOD:34 | 25 |
| N6-acetyllysine on K | UNIMOD:1 | 21 |
| Carbamyl on K | UNIMOD:5 | 20 |
| Dimethylation on K | UNIMOD:36 | 20 |
| Pyridoxal phosphate on K | UNIMOD:46 | 20 |
| Cu[I] on D | UNIMOD:531 | 17 |
| Carboxylation on E | UNIMOD:299 | 15 |
| Crotonylation on K | UNIMOD:1363 | 15 |
| Malonylation on K | UNIMOD:747 | 15 |
| Zinc on E | UNIMOD:954 | 13 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 12 |
| N-acetylthreonine on T | UNIMOD:1 | 12 |
| Carbamyl on R | UNIMOD:5 | 11 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 11 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 11 |
| N6-methyllysine on K | UNIMOD:34 | 11 |
| Butyrylation on K | UNIMOD:1289 | 10 |
| N-myristoyl glycine on G | UNIMOD:45 | 10 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 9 |
| Carboxylation on D | UNIMOD:299 | 9 |
| Trimethylation on K | UNIMOD:37 | 8 |
| Zinc on D | UNIMOD:954 | 8 |
| Glutarylation on K | UNIMOD:1848 | 7 |
| Carbamyl on M | UNIMOD:5 | 6 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Carboxylation on K | UNIMOD:299 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N6-succinyllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 4-hydroxyproline on P | UNIMOD:35 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 3 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| ADP-ribosyl glutamic acid on E | — | 2 |
| ADP-ribosylserine on S | UNIMOD:213 | 2 |
| Deamidated asparagine on N | UNIMOD:7 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| Sulfotyrosine on Y | UNIMOD:40 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
d04aaf53735d9360, written 2026-10-29T11:09:17+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