Generated summary
PXD048393 is a DDA label-free dataset (Mus musculus) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,524,774 PSMs, 76,022 peptidoforms and 6,589 protein groups, and the repository holds 56,007 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 1.52477e+06 where the producer reported 1.52489e+06 (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 1.52477e+06 where the producer reported 1.52489e+06 (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 155492 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 2 segment's accession not determinable from the sequences; 13795 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 155492 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 2 segment's accession not determinable from the sequences; 13795 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: 8947 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: 8947 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: 4 identifier(s), 4 row(s) dropped, e.g. PXD048393:F6RH57;P56654;Q6XVG2;Q91X77 written 2 times; quant_values: 60 identifier(s), 60 row(s) dropped, e.g. PXD048393:072519_SCW_VII_45_Thaxton_S1_A:label_free:protein_group:PXD048393:F6RH57;P56654;Q6XVG2;Q91X77: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: 4 identifier(s), 4 row(s) dropped, e.g. PXD048393:F6RH57;P56654;Q6XVG2;Q91X77 written 2 times; quant_values: 60 identifier(s), 60 row(s) dropped, e.g. PXD048393:072519_SCW_VII_45_Thaxton_S1_A:label_free:protein_group:PXD048393:F6RH57;P56654;Q6XVG2;Q91X77:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
151 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
151 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 | 1,524,774 |
| Peptidoforms at 1% FDR | 76,022 |
| Protein groups at 1% FDR | 6,589 |
| PTM sites | 56,007 |
| Quantitative values | 844,190 |
| PSMs, all (including decoys and sub-threshold) | 2,396,621 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 85.0% |
| 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
- 15 / 15
- 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 |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 18,039 |
| Oxidation on M | UNIMOD:35 | 8,155 |
| Deamidation on N | UNIMOD:7 | 5,619 |
| Deamidation on Q | UNIMOD:7 | 4,590 |
| Carbamyl on X | UNIMOD:5 | 1,817 |
| Fe[III] on E | UNIMOD:1870 | 1,633 |
| Hydroxylation on P | UNIMOD:35 | 1,600 |
| Fe[III] on D | UNIMOD:1870 | 1,348 |
| Citrullination on R | UNIMOD:7 | 1,305 |
| Ammonia loss on N | UNIMOD:385 | 812 |
| Hydroxylation on N | UNIMOD:35 | 788 |
| Phosphoserine on S | UNIMOD:21 | 731 |
| Fe[II] on E | UNIMOD:952 | 715 |
| Sodium on E | UNIMOD:30 | 624 |
| Fe[II] on D | UNIMOD:952 | 618 |
| Sodium on D | UNIMOD:30 | 579 |
| Ammonia loss on C | UNIMOD:385 | 421 |
| N-acetylalanine on A | UNIMOD:1 | 349 |
| Acetylation on X | UNIMOD:1 | 336 |
| Magnesium on D | UNIMOD:956 | 280 |
| Magnesium on E | UNIMOD:956 | 275 |
| Phosphorylation on S | UNIMOD:21 | 264 |
| Hydroxylation on K | UNIMOD:35 | 259 |
| Carbamyl on K | UNIMOD:5 | 246 |
| Calcium on E | UNIMOD:951 | 243 |
| Calcium on D | UNIMOD:951 | 202 |
| Methylation on K | UNIMOD:34 | 201 |
| Phosphorylation on T | UNIMOD:21 | 200 |
| Carbamyl on M | UNIMOD:5 | 198 |
| N-acetylmethionine on M | UNIMOD:1 | 191 |
| Methylation on R | UNIMOD:34 | 148 |
| Carbamyl on R | UNIMOD:5 | 138 |
| N-acetylserine on S | UNIMOD:1 | 138 |
| Water Loss on E | UNIMOD:27 | 136 |
| Formylation on K | UNIMOD:122 | 127 |
| Phosphothreonine on T | UNIMOD:21 | 119 |
| Acetylation on K | UNIMOD:1 | 117 |
| N6-acetyllysine on K | UNIMOD:1 | 113 |
| Potassium on D | UNIMOD:530 | 100 |
| Carboxylation on E | UNIMOD:299 | 91 |
| Potassium on E | UNIMOD:530 | 89 |
| Dimethylation on R | UNIMOD:36 | 85 |
| Nitrosylation on Y | UNIMOD:354 | 73 |
| Trimethylation on K | UNIMOD:37 | 69 |
| Omega-N-methylarginine on R | UNIMOD:34 | 68 |
| Carboxylation on D | UNIMOD:299 | 64 |
| Dimethylation on K | UNIMOD:36 | 62 |
| Sulfonation on Y | UNIMOD:40 | 55 |
| HexNAc on S | UNIMOD:43 | 52 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 49 |
| Carbamyl on C | UNIMOD:5 | 49 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 48 |
| 4-hydroxyproline on P | UNIMOD:35 | 45 |
| HexNAc on T | UNIMOD:43 | 45 |
| Phosphorylation on Y | UNIMOD:21 | 44 |
| Phosphotyrosine on Y | UNIMOD:21 | 41 |
| N6-methyllysine on K | UNIMOD:34 | 31 |
| N-acetylthreonine on T | UNIMOD:1 | 27 |
| Nitrosylation on C | UNIMOD:275 | 27 |
| N6-succinyllysine on K | — | 25 |
| Crotonylation on K | UNIMOD:1363 | 22 |
| N-myristoyl glycine on G | UNIMOD:45 | 19 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 19 |
| Hydroxybutyrylation on K | — | 18 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 18 |
| Carboxylation on K | UNIMOD:299 | 17 |
| Deamidated asparagine on N | UNIMOD:7 | 17 |
| Glutarylation on K | UNIMOD:1848 | 11 |
| Butyrylation on K | UNIMOD:1289 | 10 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 10 |
| N6-glutaryllysine on K | — | 8 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 8 |
| Malonylation on K | UNIMOD:747 | 6 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 6 |
| Tele-methylhistidine on H | UNIMOD:34 | 6 |
| 5-hydroxylysine on K | UNIMOD:35 | 5 |
| ADP-ribosylation on S | UNIMOD:213 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 5 |
| Glu to PyroGlu on Q | UNIMOD:28 | 5 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N5-methylglutamine on Q | UNIMOD:34 | 5 |
| N6-crotonyllysine on K | — | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N-acetylvaline on V | UNIMOD:1 | 4 |
| Succinylation on K | UNIMOD:64 | 4 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-methacryllysine on K | — | 3 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 3 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| O-palmitoleoyl serine on S | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
81243eb2e491fcc3, written 2026-10-29T11:41:24+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