Generated summary
PXD007999 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 404,489 PSMs, 39,499 peptidoforms and 4,031 protein groups, and the repository holds 20,858 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 2 for information
contaminant_label_unresolved warning
18 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: P05784, P07744, P19001, P50446, Q3TTY5.
18 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: P05784, P07744, P19001, P50446, Q3TTY5.
count_mismatch warning
The bundle holds 404489 where the producer reported 404494 (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 404489 where the producer reported 404494 (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.
high_contamination warning
61.54% of protein intensity in the worst file, 24.15% median across 30 files (DEF-QC-9 v3.5)
61.54% of protein intensity in the worst file, 24.15% median across 30 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)
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: 1499 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: 1499 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/PXD007999/02_fetch/provenance.json) with sha256 b82acddf4b45f0d260e17a1b5fef541e52fa34a008304ecae2c27a2be8a54ddb, and the file there now has 352ddd9fd6568170dc9a5044bfcdab9ee389171c18ff3fef5c043af6245c6b51: 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/PXD007999/02_fetch/provenance.json) with sha256 b82acddf4b45f0d260e17a1b5fef541e52fa34a008304ecae2c27a2be8a54ddb, and the file there now has 352ddd9fd6568170dc9a5044bfcdab9ee389171c18ff3fef5c043af6245c6b51: 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
70 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
70 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 | 404,489 |
| Peptidoforms at 1% FDR | 39,499 |
| Protein groups at 1% FDR | 4,031 |
| PTM sites | 20,858 |
| Quantitative values | 452,213 |
| PSMs, all (including decoys and sub-threshold) | 1,026,533 |
| MS2 identification rate (aging:DEF-ID-RATE) | 34.5% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 19.8% |
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
- none
- Instrument vendor
- not recorded
- Runs / samples
- 30 / 30
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000000589_AND_revi_2026-09-22_agingPTM-v1.xml
- Pipeline commit
- 19dd466d103f
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 5,456 |
| Deamidation on N | UNIMOD:7 | 1,165 |
| Carbamidomethyl on C | UNIMOD:4 | 1,152 |
| Sodium on E | UNIMOD:30 | 826 |
| Deamidation on Q | UNIMOD:7 | 675 |
| Sodium on D | UNIMOD:30 | 601 |
| Fe[III] on E | UNIMOD:1870 | 538 |
| Calcium on E | UNIMOD:951 | 436 |
| Fe[III] on D | UNIMOD:1870 | 418 |
| Hydroxylation on P | UNIMOD:35 | 392 |
| Calcium on D | UNIMOD:951 | 357 |
| Magnesium on E | UNIMOD:956 | 329 |
| Carbamyl on X | UNIMOD:5 | 323 |
| Magnesium on D | UNIMOD:956 | 270 |
| Ammonia loss on N | UNIMOD:385 | 232 |
| Fe[II] on E | UNIMOD:952 | 206 |
| Hydroxylation on N | UNIMOD:35 | 198 |
| Dimethylation on K | UNIMOD:36 | 197 |
| Acetylation on K | UNIMOD:1 | 183 |
| Potassium on E | UNIMOD:530 | 177 |
| Fe[II] on D | UNIMOD:952 | 176 |
| N-acetylalanine on A | UNIMOD:1 | 166 |
| Dimethylation on R | UNIMOD:36 | 160 |
| Potassium on D | UNIMOD:530 | 155 |
| Phosphoserine on S | UNIMOD:21 | 142 |
| Citrullination on R | UNIMOD:7 | 141 |
| Methylation on K | UNIMOD:34 | 128 |
| 4-hydroxyproline on P | UNIMOD:35 | 99 |
| Methylation on R | UNIMOD:34 | 90 |
| Hydroxylation on K | UNIMOD:35 | 87 |
| Acetylation on X | UNIMOD:1 | 80 |
| N-acetylmethionine on M | UNIMOD:1 | 77 |
| Nitrosylation on Y | UNIMOD:354 | 66 |
| N-acetylserine on S | UNIMOD:1 | 61 |
| N6-acetyllysine on K | UNIMOD:1 | 51 |
| Formylation on K | UNIMOD:122 | 49 |
| Water Loss on E | UNIMOD:27 | 46 |
| Phosphothreonine on T | UNIMOD:21 | 29 |
| Phosphorylation on S | UNIMOD:21 | 27 |
| Carbamyl on M | UNIMOD:5 | 24 |
| Sulfonation on Y | UNIMOD:40 | 24 |
| Ammonia loss on C | UNIMOD:385 | 23 |
| Omega-N-methylarginine on R | UNIMOD:34 | 22 |
| Carboxylation on E | UNIMOD:299 | 18 |
| N-acetylthreonine on T | UNIMOD:1 | 16 |
| Phosphorylation on T | UNIMOD:21 | 16 |
| Cu[I] on D | UNIMOD:531 | 15 |
| Carbamyl on K | UNIMOD:5 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| Carboxylation on D | UNIMOD:299 | 11 |
| N6-succinyllysine on K | — | 11 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 10 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| Carbamyl on R | UNIMOD:5 | 7 |
| HexNAc on T | UNIMOD:43 | 7 |
| Cu[I] on E | UNIMOD:531 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| GG (Ubiquitination Site) on K | — | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| Crotonylation on K | UNIMOD:1363 | 3 |
| HexNAc on S | UNIMOD:43 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| Trimethylation on K | UNIMOD:37 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Carboxylation on K | UNIMOD:299 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| Malonylation on K | UNIMOD:747 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| Zinc on E | UNIMOD:954 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| O-palmitoleoyl serine on S | — | 1 |
| Phosphorylation on Y | UNIMOD:21 | 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
42782f13cfd7ac91, written 2026-10-29T10:34:23+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