Generated summary
PXD034465 is a DDA label-free dataset (Mus musculus) with 19 runs, 19 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 669,101 PSMs, 51,806 peptidoforms and 4,844 protein groups, and the repository holds 22,231 PTM sites for it. 6 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, 6 warnings and 1 for information
count_mismatch warning
The bundle holds 669101 where the producer reported 669143 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 669101 where the producer reported 669143 (results.txt: All target PSMs with q-value <= 0.01 (pxreprise:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
cysteine_poor warning
0.33% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
0.33% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)
high_contamination warning
10.69% of protein intensity in the worst file, 2.17% median across 19 files (DEF-QC-9 v3.5)
10.69% of protein intensity in the worst file, 2.17% median across 19 files (DEF-QC-9 v3.5)
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 66318 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11099 site not in ptm_sites. '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 66318 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11099 site not in ptm_sites. '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: 2034 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: 2034 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.
occupancy_decoy_groups info
78 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
78 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 | 669,101 |
| Peptidoforms at 1% FDR | 51,806 |
| Protein groups at 1% FDR | 4,844 |
| PTM sites | 22,231 |
| Quantitative values | 439,004 |
| PSMs, all (including decoys and sub-threshold) | 1,452,675 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 33.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.9% |
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
- affinity_purification
- Instrument vendor
- not recorded
- Runs / samples
- 19 / 19
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2b4533e54e28
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 6,252 |
| Deamidation on Q | UNIMOD:7 | 2,707 |
| Deamidation on N | UNIMOD:7 | 2,173 |
| Citrullination on R | UNIMOD:7 | 887 |
| Hydroxylation on P | UNIMOD:35 | 758 |
| Carbamidomethyl on C | UNIMOD:4 | 649 |
| Ammonia loss on N | UNIMOD:385 | 528 |
| Sodium on E | UNIMOD:30 | 447 |
| Phosphoserine on S | UNIMOD:21 | 427 |
| Sodium on D | UNIMOD:30 | 399 |
| Hydroxylation on N | UNIMOD:35 | 362 |
| N-acetylalanine on A | UNIMOD:1 | 344 |
| Calcium on E | UNIMOD:951 | 330 |
| Calcium on D | UNIMOD:951 | 324 |
| Hydroxylation on K | UNIMOD:35 | 294 |
| Carbamyl on X | UNIMOD:5 | 293 |
| Magnesium on E | UNIMOD:956 | 262 |
| Magnesium on D | UNIMOD:956 | 258 |
| Acetylation on X | UNIMOD:1 | 251 |
| N-acetylmethionine on M | UNIMOD:1 | 203 |
| Potassium on D | UNIMOD:530 | 174 |
| Fe[II] on D | UNIMOD:952 | 157 |
| Methylation on K | UNIMOD:34 | 156 |
| Phosphorylation on S | UNIMOD:21 | 150 |
| Potassium on E | UNIMOD:530 | 142 |
| Fe[II] on E | UNIMOD:952 | 136 |
| Fe[III] on E | UNIMOD:1870 | 133 |
| N-acetylserine on S | UNIMOD:1 | 124 |
| Fe[III] on D | UNIMOD:1870 | 103 |
| Phosphorylation on T | UNIMOD:21 | 91 |
| Acetylation on K | UNIMOD:1 | 87 |
| Dimethylation on K | UNIMOD:36 | 80 |
| HexNAc on S | UNIMOD:43 | 67 |
| Methylation on R | UNIMOD:34 | 66 |
| Omega-N-methylarginine on R | UNIMOD:34 | 59 |
| N6-acetyllysine on K | UNIMOD:1 | 57 |
| Phosphothreonine on T | UNIMOD:21 | 56 |
| Dimethylation on R | UNIMOD:36 | 54 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 46 |
| Water Loss on E | UNIMOD:27 | 44 |
| Carbamyl on K | UNIMOD:5 | 43 |
| Trimethylation on K | UNIMOD:37 | 41 |
| Glutarylation on K | UNIMOD:1848 | 40 |
| Crotonylation on K | UNIMOD:1363 | 37 |
| HexNAc on T | UNIMOD:43 | 32 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 29 |
| Formylation on K | UNIMOD:122 | 29 |
| Carboxylation on E | UNIMOD:299 | 27 |
| Butyrylation on K | UNIMOD:1289 | 26 |
| Carboxylation on D | UNIMOD:299 | 26 |
| N-acetylthreonine on T | UNIMOD:1 | 26 |
| Sulfonation on Y | UNIMOD:40 | 25 |
| Carbamyl on M | UNIMOD:5 | 24 |
| Carbamyl on R | UNIMOD:5 | 24 |
| Malonylation on K | UNIMOD:747 | 24 |
| N6-succinyllysine on K | — | 21 |
| Nitrosylation on Y | UNIMOD:354 | 17 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 15 |
| Phosphorylation on Y | UNIMOD:21 | 15 |
| Phosphotyrosine on Y | UNIMOD:21 | 15 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Pyridoxal phosphate on K | UNIMOD:46 | 13 |
| Carboxylation on K | UNIMOD:299 | 12 |
| Deamidated asparagine on N | UNIMOD:7 | 11 |
| N6-glutaryllysine on K | — | 11 |
| Hydroxybutyrylation on K | — | 10 |
| Succinylation on K | UNIMOD:64 | 10 |
| 4-hydroxyproline on P | UNIMOD:35 | 9 |
| N-acetylglycine on G | UNIMOD:1 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| Carbamyl on C | UNIMOD:5 | 6 |
| Dimethylated arginine on R | UNIMOD:36 | 6 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 6 |
| Methionine (R)-sulfoxide on M | UNIMOD:35 | 5 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-methacryllysine on K | — | 4 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 3 |
| N6-malonyllysine on K | — | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| Ammonia loss on C | UNIMOD:385 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-glutamyl histamine on Q | — | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Glu to PyroGlu on Q | UNIMOD:28 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-crotonyllysine on K | — | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
94e5d5caf900551a, written 2026-10-29T09:17:00+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