Generated summary
PXD035149 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 763,140 PSMs, 29,089 peptidoforms and 3,088 protein groups, and the repository holds 25,314 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 2 for information
count_mismatch warning
The bundle holds 763140 where the producer reported 763875 (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 763140 where the producer reported 763875 (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.
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 156538 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11107 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 156538 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 11107 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: 4443 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: 4443 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), 2 row(s) dropped, e.g. PXD035149:F8VPQ6;P24822;P24823 written 3 times; quant_values: 20 identifier(s), 40 row(s) dropped, e.g. PXD035149:Service_20220209_JM_Ouimet_Sample_107:label_free:protein_group:PXD035149:F8VPQ6;P24822;P24823:QuantProject:DEF-PROT-SPC written 3 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), 2 row(s) dropped, e.g. PXD035149:F8VPQ6;P24822;P24823 written 3 times; quant_values: 20 identifier(s), 40 row(s) dropped, e.g. PXD035149:Service_20220209_JM_Ouimet_Sample_107:label_free:protein_group:PXD035149:F8VPQ6;P24822;P24823:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
292 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
292 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 | 763,140 |
| Peptidoforms at 1% FDR | 29,089 |
| Protein groups at 1% FDR | 3,088 |
| PTM sites | 25,314 |
| Quantitative values | 521,496 |
| PSMs, all (including decoys and sub-threshold) | 2,533,086 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 65.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.1% |
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
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 5,733 |
| Deamidation on N | UNIMOD:7 | 3,150 |
| Deamidation on Q | UNIMOD:7 | 2,718 |
| Oxidation on M | UNIMOD:35 | 1,496 |
| Citrullination on R | UNIMOD:7 | 1,196 |
| Hydroxylation on P | UNIMOD:35 | 896 |
| Carbamyl on X | UNIMOD:5 | 614 |
| Acetylation on K | UNIMOD:1 | 510 |
| Methylation on K | UNIMOD:34 | 482 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 443 |
| Carbamyl on M | UNIMOD:5 | 432 |
| Hydroxylation on N | UNIMOD:35 | 422 |
| Ammonia loss on N | UNIMOD:385 | 416 |
| Glutarylation on K | UNIMOD:1848 | 336 |
| Trimethylation on K | UNIMOD:37 | 303 |
| Hydroxylation on K | UNIMOD:35 | 286 |
| Magnesium on E | UNIMOD:956 | 285 |
| Magnesium on D | UNIMOD:956 | 265 |
| Sodium on E | UNIMOD:30 | 259 |
| Sodium on D | UNIMOD:30 | 233 |
| Phosphoserine on S | UNIMOD:21 | 221 |
| N-acetylalanine on A | UNIMOD:1 | 217 |
| Carbamyl on K | UNIMOD:5 | 199 |
| Acetylation on X | UNIMOD:1 | 190 |
| Methylation on R | UNIMOD:34 | 190 |
| Carboxylation on D | UNIMOD:299 | 184 |
| Calcium on D | UNIMOD:951 | 153 |
| Carboxylation on E | UNIMOD:299 | 152 |
| Dimethylation on K | UNIMOD:36 | 147 |
| Calcium on E | UNIMOD:951 | 137 |
| Phosphorylation on S | UNIMOD:21 | 136 |
| Phosphorylation on T | UNIMOD:21 | 127 |
| N6-acetyllysine on K | UNIMOD:1 | 125 |
| Water Loss on E | UNIMOD:27 | 109 |
| Formylation on K | UNIMOD:122 | 101 |
| Ammonia loss on C | UNIMOD:385 | 90 |
| Fe[II] on E | UNIMOD:952 | 87 |
| Potassium on D | UNIMOD:530 | 87 |
| Carbamyl on R | UNIMOD:5 | 84 |
| Butyrylation on K | UNIMOD:1289 | 83 |
| Succinylation on K | UNIMOD:64 | 83 |
| N-acetylserine on S | UNIMOD:1 | 81 |
| Nitrosylation on Y | UNIMOD:354 | 78 |
| Carbamyl on C | UNIMOD:5 | 77 |
| Dimethylation on R | UNIMOD:36 | 77 |
| Hydroxybutyrylation on K | — | 75 |
| HexNAc on T | UNIMOD:43 | 68 |
| Crotonylation on K | UNIMOD:1363 | 65 |
| Potassium on E | UNIMOD:530 | 65 |
| Fe[II] on D | UNIMOD:952 | 62 |
| HexNAc on S | UNIMOD:43 | 58 |
| Malonylation on K | UNIMOD:747 | 51 |
| Fe[III] on E | UNIMOD:1870 | 45 |
| N-acetylmethionine on M | UNIMOD:1 | 44 |
| Carboxylation on K | UNIMOD:299 | 42 |
| Nitrosylation on C | UNIMOD:275 | 42 |
| Fe[III] on D | UNIMOD:1870 | 41 |
| Phosphothreonine on T | UNIMOD:21 | 41 |
| 4-hydroxyproline on P | UNIMOD:35 | 37 |
| Phosphorylation on Y | UNIMOD:21 | 30 |
| Sulfonation on Y | UNIMOD:40 | 28 |
| Omega-N-methylarginine on R | UNIMOD:34 | 26 |
| N-myristoyl glycine on G | UNIMOD:45 | 25 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 24 |
| Cu[I] on E | UNIMOD:531 | 24 |
| N6-methyllysine on K | UNIMOD:34 | 24 |
| N-acetylthreonine on T | UNIMOD:1 | 21 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 21 |
| N6-succinyllysine on K | — | 21 |
| Cu[I] on D | UNIMOD:531 | 20 |
| N6-glutaryllysine on K | — | 16 |
| Deamidated asparagine on N | UNIMOD:7 | 14 |
| Pyridoxal phosphate on K | UNIMOD:46 | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| ADP-ribosylation on S | UNIMOD:213 | 8 |
| 3'-nitrotyrosine on Y | — | 7 |
| Phosphotyrosine on Y | UNIMOD:21 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Zinc on E | UNIMOD:954 | 5 |
| HexNAc on Nxt | UNIMOD:43 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| N6-methacryllysine on K | — | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
d9523efb88e5d43f, written 2026-10-29T12:05:46+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