Generated summary
PXD032202 is a DDA label-free dataset (Homo sapiens) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 183,023 PSMs, 21,771 peptidoforms and 1,925 protein groups, and the repository holds 14,088 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 183023 where the producer reported 183029 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 183023 where the producer reported 183029 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
no_design_file warning
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
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.
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: 593 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: 593 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.
upstream_provenance_changed warning
The search recorded its upstream 'db_prepare' provenance (db/provenance.json) with sha256 6c40902506a8bd4a99fe884bae6d95be46f8a1647d50570879ddcd3b3a79de59, and the file there now has 812ce696ba3f0ee2a1f79241b5e16e9267d6199f7598af77391178b825658963: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the db_prepare stage is gone unless the producer archived it.
The search recorded its upstream 'db_prepare' provenance (db/provenance.json) with sha256 6c40902506a8bd4a99fe884bae6d95be46f8a1647d50570879ddcd3b3a79de59, and the file there now has 812ce696ba3f0ee2a1f79241b5e16e9267d6199f7598af77391178b825658963: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the db_prepare stage is gone unless the producer archived it.
no_output_sdrf info
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
occupancy_decoy_groups info
293 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
293 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 | 183,023 |
| Peptidoforms at 1% FDR | 21,771 |
| Protein groups at 1% FDR | 1,925 |
| PTM sites | 14,088 |
| Quantitative values | 182,742 |
| PSMs, all (including decoys and sub-threshold) | 584,134 |
| MS2 identification rate (aging:DEF-ID-RATE) | 28.4% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 2.1% |
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
- 21 / 21
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000005640_AND_revi_2026_09_18.xml
- Pipeline commit
- 4656fb5c9edb
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 4,431 |
| Oxidation on M | UNIMOD:35 | 1,906 |
| Deamidation on N | UNIMOD:7 | 1,583 |
| Deamidation on Q | UNIMOD:7 | 1,394 |
| Hydroxylation on P | UNIMOD:35 | 648 |
| Citrullination on R | UNIMOD:7 | 427 |
| Ammonia loss on N | UNIMOD:385 | 227 |
| Sodium on E | UNIMOD:30 | 218 |
| Magnesium on E | UNIMOD:956 | 189 |
| Sodium on D | UNIMOD:30 | 189 |
| Hydroxylation on N | UNIMOD:35 | 178 |
| 4-hydroxyproline on P | UNIMOD:35 | 171 |
| Magnesium on D | UNIMOD:956 | 148 |
| N-acetylalanine on A | UNIMOD:1 | 132 |
| Ammonia loss on C | UNIMOD:385 | 131 |
| Fe[II] on E | UNIMOD:952 | 105 |
| Hydroxylation on K | UNIMOD:35 | 89 |
| Fe[II] on D | UNIMOD:952 | 87 |
| Carbamyl on X | UNIMOD:5 | 86 |
| Calcium on E | UNIMOD:951 | 81 |
| Phosphorylation on S | UNIMOD:21 | 79 |
| Formylation on K | UNIMOD:122 | 78 |
| Calcium on D | UNIMOD:951 | 63 |
| Methylation on K | UNIMOD:34 | 62 |
| N-acetylserine on S | UNIMOD:1 | 58 |
| Carbamyl on K | UNIMOD:5 | 52 |
| N-acetylmethionine on M | UNIMOD:1 | 50 |
| Phosphorylation on T | UNIMOD:21 | 49 |
| Carboxylation on E | UNIMOD:299 | 48 |
| Potassium on E | UNIMOD:530 | 46 |
| Phosphoserine on S | UNIMOD:21 | 42 |
| Water Loss on E | UNIMOD:27 | 38 |
| Acetylation on K | UNIMOD:1 | 35 |
| Fe[III] on D | UNIMOD:1870 | 35 |
| Fe[III] on E | UNIMOD:1870 | 35 |
| Methylation on R | UNIMOD:34 | 34 |
| Potassium on D | UNIMOD:530 | 32 |
| Dimethylation on K | UNIMOD:36 | 30 |
| Dimethylation on R | UNIMOD:36 | 29 |
| Carboxylation on D | UNIMOD:299 | 21 |
| N6-acetyllysine on K | UNIMOD:1 | 21 |
| Carbamyl on R | UNIMOD:5 | 20 |
| Acetylation on X | UNIMOD:1 | 18 |
| Carbamyl on M | UNIMOD:5 | 17 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| Pyridoxal phosphate on K | UNIMOD:46 | 15 |
| Carboxylation on K | UNIMOD:299 | 13 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| 5-hydroxylysine on K | UNIMOD:35 | 9 |
| Hydroxyproline on P | UNIMOD:35 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Nitrosylation on C | UNIMOD:275 | 9 |
| Phosphorylation on Y | UNIMOD:21 | 9 |
| Phosphothreonine on T | UNIMOD:21 | 9 |
| HexNAc on T | UNIMOD:43 | 8 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 7 |
| Malonylation on K | UNIMOD:747 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| Nitrosylation on Y | UNIMOD:354 | 6 |
| Sulfonation on Y | UNIMOD:40 | 6 |
| 3-hydroxyproline on P | UNIMOD:35 | 5 |
| N5-methylglutamine on Q | UNIMOD:34 | 5 |
| N6-glutaryllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Carbamyl on C | UNIMOD:5 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N6-methyllysine on K | UNIMOD:34 | 4 |
| S-methylcysteine on C | UNIMOD:34 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| Deamidated glutamine on Q | UNIMOD:7 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| HexNAc on S | UNIMOD:43 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| Phosphotyrosine on Y | UNIMOD:21 | 3 |
| Trimethylation on K | UNIMOD:37 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Hydroxybutyrylation on K | — | 2 |
| Omega-N-methylarginine on R | UNIMOD:34 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| Methionine sulfoxide on M | UNIMOD:35 | 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-nitrosocysteine on C | UNIMOD:275 | 1 |
| Sulfotyrosine on Y | UNIMOD:40 | 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
2c73cb35813984d0, written 2026-10-29T11:16:48+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