Generated summary
PXD052189 is a DDA label-free dataset (Mus musculus) with 32 runs, 32 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 15,718 PSMs, 1,752 peptidoforms and 577 protein groups, and the repository holds 1,456 PTM sites for it. 8 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, 8 warnings and 2 for information
calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)
GPTMD/search ran on uncalibrated spectra (S7)
contaminant_label_unresolved warning
10 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: Q3TTY5, Q497I4, Q61765, Q61897, Q6IFX2.
10 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: Q3TTY5, Q497I4, Q61765, Q61897, Q6IFX2.
high_contamination warning
81.31% of protein intensity in the worst file, 37.48% median across 32 files (DEF-QC-9 v3.5)
81.31% of protein intensity in the worst file, 37.48% median across 32 files (DEF-QC-9 v3.5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 15718/885703 = 1.77% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 15718/885703 = 1.77% of MS2 identified (S3)
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: 17 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: 17 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 'fetch' provenance (run_2026-09-21/PXD052189/02_fetch/provenance.json) with sha256 e47d88ea667b7e35f0ad6693c5e9670b9cbd4aac138cf76846d428758014ff9f, and the file there now has 7a504890aebc9ef50cb377233a7abbbe0809128cd05417e4c242f8fb9eae5a0c: 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 fetch stage is gone unless the producer archived it.
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD052189/02_fetch/provenance.json) with sha256 e47d88ea667b7e35f0ad6693c5e9670b9cbd4aac138cf76846d428758014ff9f, and the file there now has 7a504890aebc9ef50cb377233a7abbbe0809128cd05417e4c242f8fb9eae5a0c: 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 fetch 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
2 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
2 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 | 15,718 |
| Peptidoforms at 1% FDR | 1,752 |
| Protein groups at 1% FDR | 577 |
| PTM sites | 1,456 |
| Quantitative values | 42,297 |
| PSMs, all (including decoys and sub-threshold) | 464,166 |
| MS2 identification rate (aging:DEF-ID-RATE) | 1.8% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 26.8% |
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
- immunoprecipitation
- Instrument vendor
- not recorded
- Runs / samples
- 32 / 32
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000000589_AND_revi_2026-09-22_agingPTM-v1.xml
- Pipeline commit
- af0df8d7a2f4
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 330 |
| N-acetylalanine on A | UNIMOD:1 | 105 |
| Acetylation on X | UNIMOD:1 | 82 |
| Carbamidomethyl on C | UNIMOD:4 | 72 |
| Deamidation on N | UNIMOD:7 | 56 |
| N-acetylmethionine on M | UNIMOD:1 | 54 |
| Hydroxylation on P | UNIMOD:35 | 52 |
| Ammonia loss on N | UNIMOD:385 | 42 |
| Deamidation on Q | UNIMOD:7 | 30 |
| Carbamyl on X | UNIMOD:5 | 28 |
| Sodium on D | UNIMOD:30 | 28 |
| N-acetylserine on S | UNIMOD:1 | 27 |
| Sodium on E | UNIMOD:30 | 21 |
| Calcium on D | UNIMOD:951 | 18 |
| Fe[III] on D | UNIMOD:1870 | 18 |
| Magnesium on D | UNIMOD:956 | 18 |
| Succinylation on K | UNIMOD:64 | 15 |
| Citrullination on R | UNIMOD:7 | 14 |
| Water Loss on E | UNIMOD:27 | 14 |
| Fe[II] on D | UNIMOD:952 | 12 |
| Hydroxylation on K | UNIMOD:35 | 12 |
| Calcium on E | UNIMOD:951 | 11 |
| Hydroxylation on N | UNIMOD:35 | 11 |
| Potassium on D | UNIMOD:530 | 10 |
| N-acetylthreonine on T | UNIMOD:1 | 9 |
| Carboxylation on D | UNIMOD:299 | 8 |
| Phosphorylation on T | UNIMOD:21 | 8 |
| Ammonia loss on C | UNIMOD:385 | 7 |
| Phosphorylation on Y | UNIMOD:21 | 7 |
| Phosphoserine on S | UNIMOD:21 | 7 |
| Acetylation on K | UNIMOD:1 | 6 |
| Dimethylation on R | UNIMOD:36 | 6 |
| Fe[III] on E | UNIMOD:1870 | 6 |
| Magnesium on E | UNIMOD:956 | 6 |
| Methylation on K | UNIMOD:34 | 6 |
| Nitrosylation on Y | UNIMOD:354 | 6 |
| Fe[II] on E | UNIMOD:952 | 5 |
| Phosphorylation on S | UNIMOD:21 | 5 |
| Carboxylation on E | UNIMOD:299 | 4 |
| Dimethylation on K | UNIMOD:36 | 4 |
| Formylation on K | UNIMOD:122 | 4 |
| Pyridoxal phosphate on K | UNIMOD:46 | 4 |
| Sulfonation on Y | UNIMOD:40 | 4 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Malonylation on K | UNIMOD:747 | 3 |
| Omega-N-methylarginine on R | UNIMOD:34 | 3 |
| Potassium on E | UNIMOD:530 | 3 |
| Zinc on E | UNIMOD:954 | 3 |
| 4-hydroxyproline on P | UNIMOD:35 | 2 |
| Carbamyl on K | UNIMOD:5 | 2 |
| Carbamyl on R | UNIMOD:5 | 2 |
| Cu[I] on D | UNIMOD:531 | 2 |
| Deamidated asparagine on N | UNIMOD:7 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 2 |
| N6-acetyllysine on K | UNIMOD:1 | 2 |
| N6-methyllysine on K | UNIMOD:34 | 2 |
| Phosphothreonine on T | UNIMOD:21 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cu[I] on E | UNIMOD:531 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| Zinc on D | UNIMOD:954 | 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
8cbfda6f36c333d3, written 2026-10-29T09:16:18+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