Generated summary
PXD051715 is a DDA label-free dataset (Mus musculus) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,742,303 PSMs, 56,195 peptidoforms and 3,377 protein groups, and the repository holds 45,521 PTM sites for it. 4 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, 4 warnings and 2 for information
count_mismatch warning
The bundle holds 1.7423e+06 where the producer reported 1.74264e+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 1.7423e+06 where the producer reported 1.74264e+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.
occupancy_not_stored warning
Of 260016 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7676 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 260016 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7676 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: heart. 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: heart. 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: 6311 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: 6311 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: 5 identifier(s), 5 row(s) dropped, e.g. PXD051715:A0A088MLT8;P0DPB4 written 2 times; quant_values: 105 identifier(s), 105 row(s) dropped, e.g. PXD051715:39860_e06597_A_5_4_proteome_2h_reinj:label_free:protein_group:PXD051715:A0A088MLT8;P0DPB4: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: 5 identifier(s), 5 row(s) dropped, e.g. PXD051715:A0A088MLT8;P0DPB4 written 2 times; quant_values: 105 identifier(s), 105 row(s) dropped, e.g. PXD051715:39860_e06597_A_5_4_proteome_2h_reinj:label_free:protein_group:PXD051715:A0A088MLT8;P0DPB4:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
272 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
272 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 | 1,742,303 |
| Peptidoforms at 1% FDR | 56,195 |
| Protein groups at 1% FDR | 3,377 |
| PTM sites | 45,521 |
| Quantitative values | 784,362 |
| PSMs, all (including decoys and sub-threshold) | 2,684,937 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 109.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.5% |
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
- 21 / 21
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 9,144 |
| Deamidation on Q | UNIMOD:7 | 3,711 |
| Oxidation on M | UNIMOD:35 | 3,654 |
| Deamidation on N | UNIMOD:7 | 3,503 |
| Sodium on E | UNIMOD:30 | 1,857 |
| Hydroxylation on P | UNIMOD:35 | 1,780 |
| Sodium on D | UNIMOD:30 | 1,395 |
| Magnesium on E | UNIMOD:956 | 1,312 |
| Calcium on E | UNIMOD:951 | 1,222 |
| Carbamyl on K | UNIMOD:5 | 1,118 |
| Ammonia loss on N | UNIMOD:385 | 1,063 |
| Magnesium on D | UNIMOD:956 | 989 |
| Citrullination on R | UNIMOD:7 | 983 |
| Hydroxylation on N | UNIMOD:35 | 976 |
| Hydroxylation on K | UNIMOD:35 | 965 |
| Calcium on D | UNIMOD:951 | 932 |
| Carbamyl on X | UNIMOD:5 | 815 |
| Formylation on K | UNIMOD:122 | 715 |
| Potassium on E | UNIMOD:530 | 677 |
| Methylation on K | UNIMOD:34 | 553 |
| Potassium on D | UNIMOD:530 | 516 |
| Acetylation on K | UNIMOD:1 | 461 |
| Dimethylation on K | UNIMOD:36 | 377 |
| Phosphoserine on S | UNIMOD:21 | 375 |
| Water Loss on E | UNIMOD:27 | 339 |
| Carboxylation on E | UNIMOD:299 | 304 |
| Ammonia loss on C | UNIMOD:385 | 279 |
| N6-acetyllysine on K | UNIMOD:1 | 260 |
| Carbamyl on M | UNIMOD:5 | 255 |
| Fe[II] on E | UNIMOD:952 | 254 |
| Carboxylation on D | UNIMOD:299 | 232 |
| Fe[II] on D | UNIMOD:952 | 229 |
| Trimethylation on K | UNIMOD:37 | 211 |
| Fe[III] on E | UNIMOD:1870 | 208 |
| Methylation on R | UNIMOD:34 | 204 |
| Phosphorylation on S | UNIMOD:21 | 199 |
| Fe[III] on D | UNIMOD:1870 | 184 |
| Dimethylation on R | UNIMOD:36 | 173 |
| N-acetylalanine on A | UNIMOD:1 | 167 |
| Carboxylation on K | UNIMOD:299 | 165 |
| Phosphorylation on T | UNIMOD:21 | 154 |
| Nitrosylation on Y | UNIMOD:354 | 147 |
| Acetylation on X | UNIMOD:1 | 144 |
| Crotonylation on K | UNIMOD:1363 | 104 |
| Malonylation on K | UNIMOD:747 | 96 |
| HexNAc on S | UNIMOD:43 | 93 |
| Carbamyl on R | UNIMOD:5 | 92 |
| Phosphothreonine on T | UNIMOD:21 | 86 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 85 |
| Hydroxybutyrylation on K | — | 80 |
| N-acetylmethionine on M | UNIMOD:1 | 79 |
| N6-succinyllysine on K | — | 77 |
| HexNAc on T | UNIMOD:43 | 73 |
| N-acetylserine on S | UNIMOD:1 | 73 |
| Glutarylation on K | UNIMOD:1848 | 71 |
| Cu[I] on E | UNIMOD:531 | 66 |
| Nitrosylation on C | UNIMOD:275 | 63 |
| Carbamyl on C | UNIMOD:5 | 58 |
| Succinylation on K | UNIMOD:64 | 55 |
| 4-hydroxyproline on P | UNIMOD:35 | 53 |
| Phosphorylation on Y | UNIMOD:21 | 50 |
| Butyrylation on K | UNIMOD:1289 | 47 |
| Sulfonation on Y | UNIMOD:40 | 42 |
| Pyridoxal phosphate on K | UNIMOD:46 | 41 |
| Cu[I] on D | UNIMOD:531 | 37 |
| ADP-ribosylation on S | UNIMOD:213 | 23 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 23 |
| Omega-N-methylarginine on R | UNIMOD:34 | 23 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 22 |
| N-acetylthreonine on T | UNIMOD:1 | 20 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 20 |
| N6-methyllysine on K | UNIMOD:34 | 20 |
| N-myristoyl glycine on G | UNIMOD:45 | 19 |
| Phosphotyrosine on Y | UNIMOD:21 | 16 |
| Zinc on E | UNIMOD:954 | 15 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 13 |
| Zinc on D | UNIMOD:954 | 11 |
| HexNAc on Nxt | UNIMOD:43 | 9 |
| N6-methacryllysine on K | — | 8 |
| Citrulline on R | UNIMOD:7 | 6 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-lipoyllysine on K | UNIMOD:42 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-hydroxylysine on K | UNIMOD:35 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| Glu to PyroGlu on Q | UNIMOD:28 | 4 |
| N6-glutaryllysine on K | — | 4 |
| N6-malonyllysine on K | — | 4 |
| 3'-nitrotyrosine on Y | — | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-benzoyllysine on K | UNIMOD:136 | 3 |
| N6-biotinyllysine on K | UNIMOD:3 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 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 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
c75bed1c3adeb677, written 2026-10-29T11:42:19+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