Generated summary
PXD067102 is a DDA label-free dataset (Mus musculus) 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 1,510,240 PSMs, 48,026 peptidoforms and 5,016 protein groups, and the repository holds 45,258 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 2 for information
count_mismatch warning
The bundle holds 48026 where the producer reported 48006 (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 48026 where the producer reported 48006 (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 1.51024e+06 where the producer reported 1.5105e+06 (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 1.51024e+06 where the producer reported 1.5105e+06 (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
47.42% of protein intensity in the worst file, 12.99% median across 12 files (DEF-QC-9 v3.5)
47.42% of protein intensity in the worst file, 12.99% median across 12 files (DEF-QC-9 v3.5)
occupancy_not_stored warning
Of 157907 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9927 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 157907 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9927 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: Spleen. 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: Spleen. 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: 7919 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: 7919 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: 9 identifier(s), 12 row(s) dropped, e.g. PXD067102:A0A075B5T6;A0A0B4J1J6 written 2 times; quant_values: 109 identifier(s), 145 row(s) dropped, e.g. PXD067102:Seq67863_HFX_Young_0hr_Day1:label_free:protein_group:PXD067102:A0A075B5T6;A0A0B4J1J6: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: 9 identifier(s), 12 row(s) dropped, e.g. PXD067102:A0A075B5T6;A0A0B4J1J6 written 2 times; quant_values: 109 identifier(s), 145 row(s) dropped, e.g. PXD067102:Seq67863_HFX_Young_0hr_Day1:label_free:protein_group:PXD067102:A0A075B5T6;A0A0B4J1J6:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
174 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
174 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 | 1,510,240 |
| Peptidoforms at 1% FDR | 48,026 |
| Protein groups at 1% FDR | 5,016 |
| PTM sites | 45,258 |
| Quantitative values | 569,630 |
| PSMs, all (including decoys and sub-threshold) | 4,362,862 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 60.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 12.6% |
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
- none
- Instrument vendor
- Thermo
- Runs / samples
- 12 / 12
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0ba5e4c3fd33
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 12,283 |
| Oxidation on M | UNIMOD:35 | 4,836 |
| Deamidation on N | UNIMOD:7 | 3,118 |
| Carbamyl on K | UNIMOD:5 | 2,333 |
| Carbamyl on X | UNIMOD:5 | 2,312 |
| Deamidation on Q | UNIMOD:7 | 2,170 |
| Fe[III] on E | UNIMOD:1870 | 1,149 |
| Fe[III] on D | UNIMOD:1870 | 916 |
| Citrullination on R | UNIMOD:7 | 882 |
| Hydroxylation on P | UNIMOD:35 | 735 |
| Fe[II] on E | UNIMOD:952 | 477 |
| Ammonia loss on N | UNIMOD:385 | 424 |
| Fe[II] on D | UNIMOD:952 | 411 |
| Hydroxylation on N | UNIMOD:35 | 410 |
| Sodium on E | UNIMOD:30 | 388 |
| Carbamyl on M | UNIMOD:5 | 344 |
| N-acetylalanine on A | UNIMOD:1 | 340 |
| Methylation on K | UNIMOD:34 | 320 |
| Sodium on D | UNIMOD:30 | 310 |
| Hydroxylation on K | UNIMOD:35 | 301 |
| Acetylation on K | UNIMOD:1 | 288 |
| N6-acetyllysine on K | UNIMOD:1 | 262 |
| Carbamyl on R | UNIMOD:5 | 247 |
| Ammonia loss on C | UNIMOD:385 | 242 |
| Phosphoserine on S | UNIMOD:21 | 233 |
| Acetylation on X | UNIMOD:1 | 226 |
| Magnesium on E | UNIMOD:956 | 220 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 201 |
| Magnesium on D | UNIMOD:956 | 182 |
| Carboxylation on K | UNIMOD:299 | 141 |
| N-acetylmethionine on M | UNIMOD:1 | 134 |
| N-acetylserine on S | UNIMOD:1 | 124 |
| Calcium on D | UNIMOD:951 | 108 |
| Water Loss on E | UNIMOD:27 | 105 |
| Trimethylation on K | UNIMOD:37 | 104 |
| Phosphorylation on S | UNIMOD:21 | 101 |
| Calcium on E | UNIMOD:951 | 100 |
| Dimethylation on K | UNIMOD:36 | 87 |
| Methylation on R | UNIMOD:34 | 82 |
| Carboxylation on E | UNIMOD:299 | 78 |
| Phosphorylation on T | UNIMOD:21 | 78 |
| Formylation on K | UNIMOD:122 | 77 |
| Carboxylation on D | UNIMOD:299 | 76 |
| Malonylation on K | UNIMOD:747 | 70 |
| Succinylation on K | UNIMOD:64 | 70 |
| Carbamyl on C | UNIMOD:5 | 68 |
| Potassium on E | UNIMOD:530 | 62 |
| Glutarylation on K | UNIMOD:1848 | 61 |
| Phosphothreonine on T | UNIMOD:21 | 60 |
| N6-methyllysine on K | UNIMOD:34 | 57 |
| Omega-N-methylarginine on R | UNIMOD:34 | 57 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 52 |
| Potassium on D | UNIMOD:530 | 52 |
| Dimethylation on R | UNIMOD:36 | 50 |
| Nitrosylation on Y | UNIMOD:354 | 45 |
| Hydroxybutyrylation on K | — | 44 |
| HexNAc on S | UNIMOD:43 | 43 |
| Cu[I] on D | UNIMOD:531 | 42 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 41 |
| N6-succinyllysine on K | — | 39 |
| N6-glutaryllysine on K | — | 36 |
| HexNAc on T | UNIMOD:43 | 35 |
| Cu[I] on E | UNIMOD:531 | 33 |
| Zinc on D | UNIMOD:954 | 33 |
| Crotonylation on K | UNIMOD:1363 | 32 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 30 |
| Butyrylation on K | UNIMOD:1289 | 26 |
| N-acetylthreonine on T | UNIMOD:1 | 25 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 25 |
| Deamidated asparagine on N | UNIMOD:7 | 24 |
| Nitrosylation on C | UNIMOD:275 | 24 |
| Sulfonation on Y | UNIMOD:40 | 23 |
| 4-hydroxyproline on P | UNIMOD:35 | 21 |
| Phosphorylation on Y | UNIMOD:21 | 18 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 16 |
| N6-methacryllysine on K | — | 16 |
| Phosphotyrosine on Y | UNIMOD:21 | 15 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 13 |
| N6-crotonyllysine on K | — | 12 |
| ADP-ribosylation on S | UNIMOD:213 | 11 |
| N6-butyryllysine on K | UNIMOD:1289 | 11 |
| Pyridoxal phosphate on K | UNIMOD:46 | 10 |
| N-acetylvaline on V | UNIMOD:1 | 9 |
| Citrulline on R | UNIMOD:7 | 8 |
| N5-methylglutamine on Q | UNIMOD:34 | 8 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| Zinc on E | UNIMOD:954 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N-myristoyl glycine on G | UNIMOD:45 | 6 |
| Glu to PyroGlu on Q | UNIMOD:28 | 5 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N6-benzoyllysine on K | UNIMOD:136 | 3 |
| N6-malonyllysine on K | — | 3 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 3'-nitrotyrosine on Y | — | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
557d43f225491daa, written 2026-10-29T12:07:06+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