Generated summary
PXD042301 is a DDA label-free dataset (Mus musculus) with 31 runs, 19 samples and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 363,181 PSMs, 31,017 peptidoforms and 3,712 protein groups, and the repository holds 12,533 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 3 for information
contaminant_label_unresolved warning
15 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: P02535, P07744, P08730, P19001, Q3TTY5.
15 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: P02535, P07744, P08730, P19001, Q3TTY5.
high_contamination warning
41.99% of protein intensity in the worst file, 15.61% median across 31 files (DEF-QC-9 v3.5)
41.99% of protein intensity in the worst file, 15.61% median across 31 files (DEF-QC-9 v3.5)
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)
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: 186 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: 186 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. PXD042301:P70459;Q8R4Z4 written 2 times; quant_values: 31 identifier(s), 31 row(s) dropped, e.g. PXD042301:20210106_PHCOQEHF_PC793-OBrien_1_R1:label_free:protein_group:PXD042301:P70459;Q8R4Z4: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. PXD042301:P70459;Q8R4Z4 written 2 times; quant_values: 31 identifier(s), 31 row(s) dropped, e.g. PXD042301:20210106_PHCOQEHF_PC793-OBrien_1_R1:label_free:protein_group:PXD042301:P70459;Q8R4Z4:QuantProject:DEF-PROT-SPC 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
101 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
101 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 | 363,181 |
| Peptidoforms at 1% FDR | 31,017 |
| Protein groups at 1% FDR | 3,712 |
| PTM sites | 12,533 |
| Quantitative values | 408,611 |
| PSMs, all (including decoys and sub-threshold) | 707,975 |
| MS2 identification rate (aging:DEF-ID-RATE) | 27.5% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 12.0% |
How it was measured
- Organism searched
- Mus musculus (the protein database's organism, not a statement about the samples)
- Acquisition
- DDA
- Quantification
- label_free
- Labelling
- none
- Enrichment
- proximity_labelling
- Instrument vendor
- not recorded
- Runs / samples
- 31 / 19
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000000589_AND_revi_2026-09-22_agingPTM-v1.xml
- Pipeline commit
- 8789248ff39a
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 2,976 |
| Deamidation on N | UNIMOD:7 | 1,936 |
| Deamidation on Q | UNIMOD:7 | 1,577 |
| Hydroxylation on P | UNIMOD:35 | 492 |
| Carbamidomethyl on C | UNIMOD:4 | 466 |
| Ammonia loss on N | UNIMOD:385 | 307 |
| Citrullination on R | UNIMOD:7 | 306 |
| Carbamyl on X | UNIMOD:5 | 293 |
| Sodium on E | UNIMOD:30 | 205 |
| Hydroxylation on N | UNIMOD:35 | 198 |
| Magnesium on E | UNIMOD:956 | 177 |
| N-acetylalanine on A | UNIMOD:1 | 177 |
| Carbamyl on K | UNIMOD:5 | 173 |
| Sodium on D | UNIMOD:30 | 172 |
| Magnesium on D | UNIMOD:956 | 152 |
| Fe[II] on E | UNIMOD:952 | 142 |
| Calcium on D | UNIMOD:951 | 132 |
| Calcium on E | UNIMOD:951 | 126 |
| Fe[II] on D | UNIMOD:952 | 121 |
| Hydroxylation on K | UNIMOD:35 | 115 |
| Phosphoserine on S | UNIMOD:21 | 99 |
| Fe[III] on E | UNIMOD:1870 | 97 |
| Fe[III] on D | UNIMOD:1870 | 96 |
| Acetylation on X | UNIMOD:1 | 95 |
| N-acetylmethionine on M | UNIMOD:1 | 84 |
| N6-acetyllysine on K | UNIMOD:1 | 75 |
| Potassium on D | UNIMOD:530 | 74 |
| Formylation on K | UNIMOD:122 | 73 |
| Potassium on E | UNIMOD:530 | 64 |
| N-acetylserine on S | UNIMOD:1 | 60 |
| 4-hydroxyproline on P | UNIMOD:35 | 56 |
| Carboxylation on E | UNIMOD:299 | 55 |
| Phosphorylation on S | UNIMOD:21 | 53 |
| Water Loss on E | UNIMOD:27 | 42 |
| Methylation on K | UNIMOD:34 | 31 |
| Carboxylation on D | UNIMOD:299 | 30 |
| Carboxylation on K | UNIMOD:299 | 30 |
| Cu[I] on E | UNIMOD:531 | 30 |
| Phosphorylation on T | UNIMOD:21 | 30 |
| Acetylation on K | UNIMOD:1 | 27 |
| Carbamyl on M | UNIMOD:5 | 27 |
| Nitrosylation on Y | UNIMOD:354 | 26 |
| Dimethylation on K | UNIMOD:36 | 24 |
| Methylation on R | UNIMOD:34 | 24 |
| Cu[I] on D | UNIMOD:531 | 19 |
| N6-succinyllysine on K | — | 19 |
| N-acetylthreonine on T | UNIMOD:1 | 17 |
| Carbamyl on R | UNIMOD:5 | 16 |
| N6-glutaryllysine on K | — | 16 |
| Phosphothreonine on T | UNIMOD:21 | 15 |
| Sulfonation on Y | UNIMOD:40 | 15 |
| Dimethylation on R | UNIMOD:36 | 14 |
| Succinylation on K | UNIMOD:64 | 14 |
| Ammonia loss on C | UNIMOD:385 | 13 |
| Phosphorylation on Y | UNIMOD:21 | 13 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 12 |
| Zinc on E | UNIMOD:954 | 12 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 11 |
| Trimethylation on K | UNIMOD:37 | 10 |
| Deamidated asparagine on N | UNIMOD:7 | 9 |
| Malonylation on K | UNIMOD:747 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 9 |
| Pyridoxal phosphate on K | UNIMOD:46 | 8 |
| Zinc on D | UNIMOD:954 | 8 |
| HexNAc on S | UNIMOD:43 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| Omega-N-methylarginine on R | UNIMOD:34 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| Crotonylation on K | UNIMOD:1363 | 5 |
| HexNAc on T | UNIMOD:43 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N6-methyllysine on K | UNIMOD:34 | 5 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Citrulline on R | UNIMOD:7 | 3 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| N-acetylproline on P | UNIMOD:1 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| N6-methacryllysine on K | — | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| Hydroxybutyrylation on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| N6-malonyllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
55abb8c222f7d4b9, written 2026-10-29T10:57:00+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