Generated summary
PXD015079 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 261,188 PSMs, 31,951 peptidoforms and 2,689 protein groups, and the repository holds 11,932 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 261188 where the producer reported 261245 (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 261188 where the producer reported 261245 (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.
cysteine_poor warning
2.90% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
2.90% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
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 40135 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 segment's accession not determinable from the sequences; 3792 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 40135 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 segment's accession not determinable from the sequences; 3792 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: 731 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: 731 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. PXD015079:Q5TCY1;Q6IQ55 written 2 times; quant_values: 12 identifier(s), 12 row(s) dropped, e.g. PXD015079:190319-Labrie-3366-APP:label_free:protein_group:PXD015079:Q5TCY1;Q6IQ55: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. PXD015079:Q5TCY1;Q6IQ55 written 2 times; quant_values: 12 identifier(s), 12 row(s) dropped, e.g. PXD015079:190319-Labrie-3366-APP:label_free:protein_group:PXD015079:Q5TCY1;Q6IQ55:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
44 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
44 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 | 261,188 |
| Peptidoforms at 1% FDR | 31,951 |
| Protein groups at 1% FDR | 2,689 |
| PTM sites | 11,932 |
| Quantitative values | 224,548 |
| PSMs, all (including decoys and sub-threshold) | 626,680 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 43.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.5% |
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
- 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
- 089bcc7b11dc
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Deamidation on N | UNIMOD:7 | 2,385 |
| Deamidation on Q | UNIMOD:7 | 1,889 |
| Oxidation on M | UNIMOD:35 | 917 |
| Ammonia loss on N | UNIMOD:385 | 549 |
| Hydroxylation on P | UNIMOD:35 | 541 |
| Citrullination on R | UNIMOD:7 | 528 |
| Magnesium on D | UNIMOD:956 | 254 |
| Magnesium on E | UNIMOD:956 | 232 |
| Hydroxylation on N | UNIMOD:35 | 221 |
| Hydroxylation on K | UNIMOD:35 | 216 |
| Sodium on E | UNIMOD:30 | 205 |
| Fe[II] on E | UNIMOD:952 | 191 |
| Fe[II] on D | UNIMOD:952 | 184 |
| N-acetylalanine on A | UNIMOD:1 | 174 |
| Methylation on K | UNIMOD:34 | 168 |
| Sodium on D | UNIMOD:30 | 167 |
| Fe[III] on D | UNIMOD:1870 | 149 |
| Phosphoserine on S | UNIMOD:21 | 143 |
| Phosphorylation on S | UNIMOD:21 | 135 |
| Phosphorylation on T | UNIMOD:21 | 126 |
| Fe[III] on E | UNIMOD:1870 | 106 |
| Acetylation on X | UNIMOD:1 | 99 |
| Acetylation on K | UNIMOD:1 | 95 |
| Water Loss on E | UNIMOD:27 | 95 |
| Calcium on D | UNIMOD:951 | 89 |
| Methylation on R | UNIMOD:34 | 87 |
| Carbamyl on X | UNIMOD:5 | 85 |
| Calcium on E | UNIMOD:951 | 81 |
| Dimethylation on K | UNIMOD:36 | 78 |
| N-acetylmethionine on M | UNIMOD:1 | 72 |
| N-acetylserine on S | UNIMOD:1 | 72 |
| Formylation on K | UNIMOD:122 | 57 |
| Sulfonation on Y | UNIMOD:40 | 47 |
| Trimethylation on K | UNIMOD:37 | 47 |
| 4-hydroxyproline on P | UNIMOD:35 | 45 |
| Carbamyl on K | UNIMOD:5 | 44 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 44 |
| N6-acetyllysine on K | UNIMOD:1 | 43 |
| Dimethylation on R | UNIMOD:36 | 39 |
| Carboxylation on E | UNIMOD:299 | 36 |
| HexNAc on T | UNIMOD:43 | 35 |
| Glutarylation on K | UNIMOD:1848 | 34 |
| Hydroxybutyrylation on K | — | 34 |
| Crotonylation on K | UNIMOD:1363 | 33 |
| Potassium on D | UNIMOD:530 | 32 |
| Carboxylation on D | UNIMOD:299 | 31 |
| Potassium on E | UNIMOD:530 | 31 |
| Malonylation on K | UNIMOD:747 | 30 |
| Phosphothreonine on T | UNIMOD:21 | 29 |
| Butyrylation on K | UNIMOD:1289 | 27 |
| Nitrosylation on Y | UNIMOD:354 | 27 |
| Succinylation on K | UNIMOD:64 | 27 |
| Cu[I] on D | UNIMOD:531 | 25 |
| HexNAc on S | UNIMOD:43 | 23 |
| N-acetylthreonine on T | UNIMOD:1 | 22 |
| Nitrosylation on C | UNIMOD:275 | 21 |
| Phosphorylation on Y | UNIMOD:21 | 19 |
| Cu[I] on E | UNIMOD:531 | 18 |
| Omega-N-methylarginine on R | UNIMOD:34 | 17 |
| Citrulline on R | UNIMOD:7 | 16 |
| Carbamyl on R | UNIMOD:5 | 15 |
| N-myristoyl glycine on G | UNIMOD:45 | 15 |
| Ammonia loss on C | UNIMOD:385 | 12 |
| Carbamyl on C | UNIMOD:5 | 12 |
| Carboxylation on K | UNIMOD:299 | 12 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| N6-methyllysine on K | UNIMOD:34 | 12 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 12 |
| Carbamyl on M | UNIMOD:5 | 11 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 11 |
| N6-succinyllysine on K | — | 11 |
| N-acetylglycine on G | UNIMOD:1 | 10 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 9 |
| Pyridoxal phosphate on K | UNIMOD:46 | 9 |
| N-acetylvaline on V | UNIMOD:1 | 8 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 7 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| Zinc on E | UNIMOD:954 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Zinc on D | UNIMOD:954 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Deamidated glutamine on Q | UNIMOD:7 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N-pyruvate 2-iminyl-valine on V | UNIMOD:422 | 2 |
| S-glutathionyl cysteine on C | UNIMOD:55 | 2 |
| Cysteine methyl ester on C | UNIMOD:34 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| N6-methacryllysine on K | — | 1 |
| O-(pantetheine 4'-phosphoryl)serine on S | UNIMOD:49 | 1 |
| S-cysteinyl cysteine on C | UNIMOD:312 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
e1c15be2f29acb64, written 2026-10-29T11:11:23+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