Generated summary
PXD032040 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 118,909 PSMs, 21,185 peptidoforms and 2,538 protein groups, and the repository holds 9,604 PTM sites for it. 7 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, 7 warnings and 3 for information
contaminant_label_unresolved warning
16 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: P01008, P02533, P08729, P12035, P19013.
16 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: P01008, P02533, P08729, P12035, P19013.
high_contamination warning
31.48% of protein intensity in the worst file, 5.38% median across 15 files (DEF-QC-9 v2)
31.48% of protein intensity in the worst file, 5.38% median across 15 files (DEF-QC-9 v2)
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.
occupancy_not_stored warning
Of 30098 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 40 segment's accession not determinable from the sequences. '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 30098 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 40 segment's accession not determinable from the sequences. '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: 747 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; 31 named a protein the searched databases carry with different sequences, where the search's TCAmbiguity does not say which one it searched (O76011, P19013). 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: 747 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; 31 named a protein the searched databases carry with different sequences, where the search's TCAmbiguity does not say which one it searched (O76011, P19013). 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.
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. PXD032040:A8MPP1;Q92771;Q96FC9 written 2 times; quant_values: 17 identifier(s), 17 row(s) dropped, e.g. PXD032040:20161028_AWH_ColID_236_ProjectID_240_Deniz_Kurian_IgG1:label_free:protein_group:PXD032040:A8MPP1;Q92771;Q96FC9:QuantProject:DEF-PROT-INT 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. PXD032040:A8MPP1;Q92771;Q96FC9 written 2 times; quant_values: 17 identifier(s), 17 row(s) dropped, e.g. PXD032040:20161028_AWH_ColID_236_ProjectID_240_Deniz_Kurian_IgG1:label_free:protein_group:PXD032040:A8MPP1;Q92771;Q96FC9:QuantProject:DEF-PROT-INT written 2 times. The full list is in bundle.json under collapsed_duplicates.
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
53 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
53 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 | 118,909 |
| Peptidoforms at 1% FDR | 21,185 |
| Protein groups at 1% FDR | 2,538 |
| PTM sites | 9,604 |
| Quantitative values | 218,505 |
| PSMs, all (including decoys and sub-threshold) | 234,986 |
| MS2 identification rate (aging:DEF-ID-RATE) | 44.4% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 8.0% |
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
- immunoprecipitation
- Instrument vendor
- not recorded
- Runs / samples
- 15 / 15
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000005640_AND_revi_2026_09_18.xml
- Pipeline commit
- 1c5a980c4349
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 2,811 |
| Deamidation on Q | UNIMOD:7 | 1,747 |
| Oxidation on M | UNIMOD:35 | 1,477 |
| Deamidation on N | UNIMOD:7 | 992 |
| Citrullination on R | UNIMOD:7 | 283 |
| Carbamyl on X | UNIMOD:5 | 241 |
| N-acetylalanine on A | UNIMOD:1 | 143 |
| Ammonia loss on N | UNIMOD:385 | 108 |
| Ammonia loss on C | UNIMOD:385 | 89 |
| Glutarylation on K | UNIMOD:1848 | 69 |
| Phosphoserine on S | UNIMOD:21 | 60 |
| N-acetylserine on S | UNIMOD:1 | 49 |
| Carbamyl on K | UNIMOD:5 | 47 |
| Hydroxylation on N | UNIMOD:35 | 30 |
| Fe[III] on E | UNIMOD:1870 | 26 |
| N-acetylmethionine on M | UNIMOD:1 | 24 |
| Sodium on E | UNIMOD:30 | 24 |
| Fe[III] on D | UNIMOD:1870 | 23 |
| Hydroxylation on K | UNIMOD:35 | 23 |
| Calcium on E | UNIMOD:951 | 21 |
| Hydroxylation on P | UNIMOD:35 | 21 |
| Calcium on D | UNIMOD:951 | 19 |
| Sodium on D | UNIMOD:30 | 19 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 18 |
| N6-acetyllysine on K | UNIMOD:1 | 18 |
| Water Loss on E | UNIMOD:27 | 18 |
| N6-glutaryllysine on K | — | 15 |
| Methylation on K | UNIMOD:34 | 14 |
| N-acetylthreonine on T | UNIMOD:1 | 14 |
| Omega-N-methylarginine on R | UNIMOD:34 | 14 |
| Phosphothreonine on T | UNIMOD:21 | 14 |
| Methylation on R | UNIMOD:34 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 13 |
| N6-malonyllysine on K | — | 12 |
| N6-methyllysine on K | UNIMOD:34 | 12 |
| Acetylation on K | UNIMOD:1 | 11 |
| Acetylation on X | UNIMOD:1 | 11 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 11 |
| Carbamyl on M | UNIMOD:5 | 9 |
| Nitrosylation on Y | UNIMOD:354 | 9 |
| Carbamyl on R | UNIMOD:5 | 8 |
| Carboxylation on K | UNIMOD:299 | 8 |
| Trimethylation on K | UNIMOD:37 | 8 |
| Dimethylation on R | UNIMOD:36 | 6 |
| Magnesium on E | UNIMOD:956 | 6 |
| Potassium on E | UNIMOD:530 | 6 |
| Carboxylation on E | UNIMOD:299 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 5 |
| Dimethylation on K | UNIMOD:36 | 5 |
| Fe[II] on D | UNIMOD:952 | 5 |
| Fe[II] on E | UNIMOD:952 | 5 |
| Magnesium on D | UNIMOD:956 | 5 |
| Citrulline on R | UNIMOD:7 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-methacryllysine on K | — | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Formylation on K | UNIMOD:122 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-succinyllysine on K | — | 2 |
| Potassium on D | UNIMOD:530 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Carboxylation on D | UNIMOD:299 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| Methionine sulfoxide on M | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
9fc77a7432a39d91, written 2026-10-29T09:33:14+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group