Generated summary
PXD041139 is a DDA label-free dataset (Homo sapiens) with 14 runs, 14 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 432,972 PSMs, 8,062 peptidoforms and 492 protein groups, and the repository holds 10,811 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 432972 where the producer reported 433089 (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 432972 where the producer reported 433089 (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.
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 76483 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6 duplicate entry for one site and run (identical values; same protein group); 29 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 76483 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 6 duplicate entry for one site and run (identical values; same protein group); 29 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: 3102 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: 3102 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: 2 identifier(s), 2 row(s) dropped, e.g. PXD041139:P00325;P00326;P07327 written 2 times; quant_values: 28 identifier(s), 28 row(s) dropped, e.g. PXD041139:22060212_WS_AFF2:label_free:protein_group:PXD041139:P00325;P00326;P07327: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: 2 identifier(s), 2 row(s) dropped, e.g. PXD041139:P00325;P00326;P07327 written 2 times; quant_values: 28 identifier(s), 28 row(s) dropped, e.g. PXD041139:22060212_WS_AFF2:label_free:protein_group:PXD041139:P00325;P00326;P07327:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
108 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
108 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 | 432,972 |
| Peptidoforms at 1% FDR | 8,062 |
| Protein groups at 1% FDR | 492 |
| PTM sites | 10,811 |
| Quantitative values | 107,422 |
| PSMs, all (including decoys and sub-threshold) | 1,533,561 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 29.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.1% |
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
- 14 / 14
- 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 | 1,216 |
| Deamidation on Q | UNIMOD:7 | 933 |
| Oxidation on M | UNIMOD:35 | 802 |
| Deamidation on N | UNIMOD:7 | 754 |
| Fe[III] on E | UNIMOD:1870 | 576 |
| Fe[II] on E | UNIMOD:952 | 453 |
| Sodium on E | UNIMOD:30 | 444 |
| Hydroxylation on P | UNIMOD:35 | 411 |
| Magnesium on E | UNIMOD:956 | 407 |
| Fe[III] on D | UNIMOD:1870 | 383 |
| Fe[II] on D | UNIMOD:952 | 338 |
| Magnesium on D | UNIMOD:956 | 304 |
| Sodium on D | UNIMOD:30 | 297 |
| Ammonia loss on N | UNIMOD:385 | 259 |
| Calcium on E | UNIMOD:951 | 212 |
| Citrullination on R | UNIMOD:7 | 208 |
| Hydroxylation on N | UNIMOD:35 | 181 |
| Methylation on R | UNIMOD:34 | 179 |
| Calcium on D | UNIMOD:951 | 162 |
| Methylation on K | UNIMOD:34 | 144 |
| Potassium on E | UNIMOD:530 | 137 |
| Carbamyl on X | UNIMOD:5 | 119 |
| Hydroxylation on K | UNIMOD:35 | 108 |
| Water Loss on E | UNIMOD:27 | 104 |
| Carboxylation on E | UNIMOD:299 | 97 |
| Potassium on D | UNIMOD:530 | 85 |
| Trimethylation on K | UNIMOD:37 | 82 |
| Formylation on K | UNIMOD:122 | 81 |
| Cu[I] on E | UNIMOD:531 | 73 |
| Dimethylation on R | UNIMOD:36 | 71 |
| Acetylation on K | UNIMOD:1 | 56 |
| Cu[I] on D | UNIMOD:531 | 56 |
| Phosphoserine on S | UNIMOD:21 | 56 |
| Nitrosylation on Y | UNIMOD:354 | 48 |
| Dimethylation on K | UNIMOD:36 | 46 |
| Zinc on E | UNIMOD:954 | 44 |
| Carbamyl on K | UNIMOD:5 | 41 |
| Phosphorylation on S | UNIMOD:21 | 41 |
| Carboxylation on D | UNIMOD:299 | 38 |
| ADP-ribosylation on S | UNIMOD:213 | 36 |
| Carbamyl on M | UNIMOD:5 | 30 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 23 |
| Carboxylation on K | UNIMOD:299 | 19 |
| HexNAc on T | UNIMOD:43 | 19 |
| Glutarylation on K | UNIMOD:1848 | 18 |
| Carbamyl on C | UNIMOD:5 | 17 |
| N6-acetyllysine on K | UNIMOD:1 | 17 |
| Ammonia loss on C | UNIMOD:385 | 16 |
| Butyrylation on K | UNIMOD:1289 | 16 |
| Phosphothreonine on T | UNIMOD:21 | 15 |
| Phosphorylation on T | UNIMOD:21 | 14 |
| Crotonylation on K | UNIMOD:1363 | 13 |
| HexNAc on S | UNIMOD:43 | 13 |
| Nitrosylation on C | UNIMOD:275 | 13 |
| 4-hydroxyproline on P | UNIMOD:35 | 12 |
| Carbamyl on R | UNIMOD:5 | 12 |
| Hydroxybutyrylation on K | — | 10 |
| Zinc on D | UNIMOD:954 | 10 |
| Pyridoxal phosphate on K | UNIMOD:46 | 7 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| Phosphorylation on Y | UNIMOD:21 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| Sulfonation on Y | UNIMOD:40 | 5 |
| Hydroxyproline on P | UNIMOD:35 | 4 |
| Malonylation on K | UNIMOD:747 | 4 |
| N6-succinyllysine on K | — | 4 |
| Omega-N-methylarginine on R | UNIMOD:34 | 4 |
| Acetylation on X | UNIMOD:1 | 3 |
| N-acetylserine on S | UNIMOD:1 | 3 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 2 |
| N-acetylalanine on A | UNIMOD:1 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Deamidated asparagine on N | UNIMOD:7 | 1 |
| N-acetylthreonine on T | UNIMOD:1 | 1 |
| N-acetylvaline on V | UNIMOD:1 | 1 |
| S-cysteinyl cysteine on C | UNIMOD:312 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
b68e502cff1a1bf9, written 2026-10-29T09:13:28+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