Generated summary
PXD075372 is a DDA label-free dataset (Homo sapiens) with 24 runs, 24 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,107,679 PSMs, 77,281 peptidoforms and 6,036 protein groups, and the repository holds 73,987 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 1.10768e+06 where the producer reported 1.10907e+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 1.10768e+06 where the producer reported 1.10907e+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.
low_core_use warning
14.08 avg cores of 32 allowed (S5)
14.08 avg cores of 32 allowed (S5)
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 259465 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 13304 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 259465 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 13304 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: 4193 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: 4193 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: 3 identifier(s), 3 row(s) dropped, e.g. PXD075372:A0A1B0GTS1;A0A1B0GWH4 written 2 times; quant_values: 72 identifier(s), 72 row(s) dropped, e.g. PXD075372:QEX03_AM_230117_CW10_065.raw.thermo:label_free:protein_group:PXD075372:A0A1B0GTS1;A0A1B0GWH4: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: 3 identifier(s), 3 row(s) dropped, e.g. PXD075372:A0A1B0GTS1;A0A1B0GWH4 written 2 times; quant_values: 72 identifier(s), 72 row(s) dropped, e.g. PXD075372:QEX03_AM_230117_CW10_065.raw.thermo:label_free:protein_group:PXD075372:A0A1B0GTS1;A0A1B0GWH4:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
285 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
285 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 | 1,107,679 |
| Peptidoforms at 1% FDR | 77,281 |
| Protein groups at 1% FDR | 6,036 |
| PTM sites | 73,987 |
| Quantitative values | 896,131 |
| PSMs, all (including decoys and sub-threshold) | 1,559,413 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 77.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.8% |
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
- 24 / 24
- 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 | 16,246 |
| Deamidation on Q | UNIMOD:7 | 9,454 |
| Deamidation on N | UNIMOD:7 | 8,893 |
| Oxidation on M | UNIMOD:35 | 5,404 |
| Citrullination on R | UNIMOD:7 | 3,888 |
| Magnesium on E | UNIMOD:956 | 2,636 |
| Sodium on E | UNIMOD:30 | 2,596 |
| Carbamyl on X | UNIMOD:5 | 2,308 |
| Sodium on D | UNIMOD:30 | 2,152 |
| Magnesium on D | UNIMOD:956 | 2,112 |
| Calcium on E | UNIMOD:951 | 2,030 |
| Calcium on D | UNIMOD:951 | 1,755 |
| Hydroxylation on P | UNIMOD:35 | 1,506 |
| Ammonia loss on N | UNIMOD:385 | 1,426 |
| Potassium on E | UNIMOD:530 | 987 |
| Potassium on D | UNIMOD:530 | 908 |
| Hydroxylation on N | UNIMOD:35 | 751 |
| Ammonia loss on C | UNIMOD:385 | 581 |
| Phosphoserine on S | UNIMOD:21 | 415 |
| Methylation on K | UNIMOD:34 | 400 |
| Hydroxylation on K | UNIMOD:35 | 363 |
| N-acetylalanine on A | UNIMOD:1 | 337 |
| Methylation on R | UNIMOD:34 | 333 |
| Carboxylation on E | UNIMOD:299 | 309 |
| Carbamyl on K | UNIMOD:5 | 302 |
| Carboxylation on D | UNIMOD:299 | 281 |
| Carbamyl on M | UNIMOD:5 | 263 |
| Acetylation on K | UNIMOD:1 | 262 |
| Dimethylation on R | UNIMOD:36 | 259 |
| Dimethylation on K | UNIMOD:36 | 252 |
| Carbamyl on R | UNIMOD:5 | 247 |
| Formylation on K | UNIMOD:122 | 238 |
| N-acetylmethionine on M | UNIMOD:1 | 202 |
| Water Loss on E | UNIMOD:27 | 199 |
| Acetylation on X | UNIMOD:1 | 155 |
| N6-acetyllysine on K | UNIMOD:1 | 147 |
| Trimethylation on K | UNIMOD:37 | 135 |
| Fe[II] on E | UNIMOD:952 | 131 |
| Nitrosylation on Y | UNIMOD:354 | 125 |
| Phosphorylation on S | UNIMOD:21 | 125 |
| N-acetylserine on S | UNIMOD:1 | 117 |
| Phosphothreonine on T | UNIMOD:21 | 105 |
| Fe[II] on D | UNIMOD:952 | 104 |
| Carbamyl on C | UNIMOD:5 | 102 |
| Phosphorylation on T | UNIMOD:21 | 91 |
| Cu[I] on E | UNIMOD:531 | 76 |
| Fe[III] on D | UNIMOD:1870 | 76 |
| HexNAc on T | UNIMOD:43 | 73 |
| Fe[III] on E | UNIMOD:1870 | 71 |
| Carboxylation on K | UNIMOD:299 | 70 |
| Malonylation on K | UNIMOD:747 | 70 |
| Nitrosylation on C | UNIMOD:275 | 70 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 67 |
| Crotonylation on K | UNIMOD:1363 | 66 |
| Cu[I] on D | UNIMOD:531 | 64 |
| HexNAc on S | UNIMOD:43 | 58 |
| Omega-N-methylarginine on R | UNIMOD:34 | 56 |
| Butyrylation on K | UNIMOD:1289 | 45 |
| Hydroxybutyrylation on K | — | 44 |
| 4-hydroxyproline on P | UNIMOD:35 | 41 |
| Glutarylation on K | UNIMOD:1848 | 41 |
| Zinc on E | UNIMOD:954 | 40 |
| Succinylation on K | UNIMOD:64 | 38 |
| Zinc on D | UNIMOD:954 | 36 |
| N6-succinyllysine on K | — | 32 |
| Phosphorylation on Y | UNIMOD:21 | 26 |
| Phosphotyrosine on Y | UNIMOD:21 | 26 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 21 |
| N-acetylthreonine on T | UNIMOD:1 | 21 |
| Sulfonation on Y | UNIMOD:40 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 17 |
| N6-methyllysine on K | UNIMOD:34 | 15 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 14 |
| N6-methacryllysine on K | — | 12 |
| N6-glutaryllysine on K | — | 11 |
| ADP-ribosylation on S | UNIMOD:213 | 10 |
| Hydroxyproline on P | UNIMOD:35 | 9 |
| N-acetylglycine on G | UNIMOD:1 | 9 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 7 |
| Pyridoxal phosphate on K | UNIMOD:46 | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| 3'-nitrotyrosine on Y | — | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N-myristoyl glycine on G | UNIMOD:45 | 5 |
| N6-crotonyllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 4 |
| N6-malonyllysine on K | — | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| ADP-ribosylcysteine on C | UNIMOD:213 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| (3S)-3-hydroxyaspartate on D | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Glu to PyroGlu on Q | UNIMOD:28 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N4,N4-dimethylasparagine on N | UNIMOD:36 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| Phosphohistidine on H | UNIMOD:21 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
9e58f7b2a83da02c, written 2026-10-29T12:08:33+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