Generated summary
PXD019849 is a DDA label-free dataset (Mus musculus) with 10 runs, 10 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 668,514 PSMs, 68,501 peptidoforms and 5,975 protein groups, and the repository holds 30,700 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 668514 where the producer reported 668797 (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 668514 where the producer reported 668797 (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 93022 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9258 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 93022 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9258 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: 1666 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: 1666 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: 2 identifier(s), 3 row(s) dropped, e.g. PXD019849:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KEA6 written 3 times; quant_values: 20 identifier(s), 30 row(s) dropped, e.g. PXD019849:190119_FS1_Li_Hage_KO_145:label_free:protein_group:PXD019849:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KEA6: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: 2 identifier(s), 3 row(s) dropped, e.g. PXD019849:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KEA6 written 3 times; quant_values: 20 identifier(s), 30 row(s) dropped, e.g. PXD019849:190119_FS1_Li_Hage_KO_145:label_free:protein_group:PXD019849:A0A9L6KDT8;A0A9L6KDV4;A0A9L6KEA6:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
79 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
79 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 | 668,514 |
| Peptidoforms at 1% FDR | 68,501 |
| Protein groups at 1% FDR | 5,975 |
| PTM sites | 30,700 |
| Quantitative values | 552,319 |
| PSMs, all (including decoys and sub-threshold) | 853,148 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 72.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.2% |
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
- 10 / 10
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 089bcc7b11dc
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 8,790 |
| Deamidation on Q | UNIMOD:7 | 4,044 |
| Deamidation on N | UNIMOD:7 | 3,823 |
| Oxidation on M | UNIMOD:35 | 2,532 |
| Citrullination on R | UNIMOD:7 | 826 |
| Hydroxylation on P | UNIMOD:35 | 774 |
| Sodium on E | UNIMOD:30 | 666 |
| Magnesium on E | UNIMOD:956 | 637 |
| Phosphoserine on S | UNIMOD:21 | 582 |
| Sodium on D | UNIMOD:30 | 533 |
| Magnesium on D | UNIMOD:956 | 498 |
| Ammonia loss on N | UNIMOD:385 | 469 |
| N-acetylalanine on A | UNIMOD:1 | 328 |
| Calcium on E | UNIMOD:951 | 327 |
| Acetylation on X | UNIMOD:1 | 325 |
| Hydroxylation on N | UNIMOD:35 | 300 |
| Calcium on D | UNIMOD:951 | 297 |
| Hydroxylation on K | UNIMOD:35 | 229 |
| Phosphorylation on S | UNIMOD:21 | 228 |
| Methylation on K | UNIMOD:34 | 224 |
| Potassium on E | UNIMOD:530 | 216 |
| Fe[III] on E | UNIMOD:1870 | 201 |
| Fe[III] on D | UNIMOD:1870 | 195 |
| Potassium on D | UNIMOD:530 | 195 |
| N-acetylmethionine on M | UNIMOD:1 | 154 |
| Carbamyl on X | UNIMOD:5 | 148 |
| Phosphorylation on T | UNIMOD:21 | 143 |
| Water Loss on E | UNIMOD:27 | 141 |
| Fe[II] on E | UNIMOD:952 | 127 |
| Fe[II] on D | UNIMOD:952 | 126 |
| N-acetylserine on S | UNIMOD:1 | 123 |
| Ammonia loss on C | UNIMOD:385 | 118 |
| N6-acetyllysine on K | UNIMOD:1 | 115 |
| Phosphothreonine on T | UNIMOD:21 | 107 |
| Trimethylation on K | UNIMOD:37 | 106 |
| Methylation on R | UNIMOD:34 | 96 |
| Dimethylation on K | UNIMOD:36 | 89 |
| Carbamyl on K | UNIMOD:5 | 87 |
| Acetylation on K | UNIMOD:1 | 86 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 80 |
| HexNAc on T | UNIMOD:43 | 75 |
| Dimethylation on R | UNIMOD:36 | 67 |
| Formylation on K | UNIMOD:122 | 67 |
| HexNAc on S | UNIMOD:43 | 67 |
| Omega-N-methylarginine on R | UNIMOD:34 | 58 |
| Carbamyl on M | UNIMOD:5 | 55 |
| Carboxylation on E | UNIMOD:299 | 54 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 51 |
| Malonylation on K | UNIMOD:747 | 47 |
| Butyrylation on K | UNIMOD:1289 | 42 |
| Glutarylation on K | UNIMOD:1848 | 38 |
| Nitrosylation on Y | UNIMOD:354 | 33 |
| Crotonylation on K | UNIMOD:1363 | 32 |
| Carboxylation on D | UNIMOD:299 | 30 |
| Succinylation on K | UNIMOD:64 | 30 |
| Carboxylation on K | UNIMOD:299 | 29 |
| Hydroxybutyrylation on K | — | 28 |
| Phosphorylation on Y | UNIMOD:21 | 27 |
| Carbamyl on C | UNIMOD:5 | 26 |
| Carbamyl on R | UNIMOD:5 | 26 |
| Deamidated asparagine on N | UNIMOD:7 | 25 |
| N-acetylthreonine on T | UNIMOD:1 | 24 |
| 4-hydroxyproline on P | UNIMOD:35 | 23 |
| N6-succinyllysine on K | — | 23 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 22 |
| N6-methyllysine on K | UNIMOD:34 | 22 |
| Nitrosylation on C | UNIMOD:275 | 22 |
| Cu[I] on E | UNIMOD:531 | 21 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 18 |
| Phosphotyrosine on Y | UNIMOD:21 | 17 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| N6-glutaryllysine on K | — | 16 |
| Sulfonation on Y | UNIMOD:40 | 16 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 15 |
| Cu[I] on D | UNIMOD:531 | 14 |
| Pyridoxal phosphate on K | UNIMOD:46 | 12 |
| N-myristoyl glycine on G | UNIMOD:45 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 9 |
| N6-crotonyllysine on K | — | 9 |
| Zinc on E | UNIMOD:954 | 7 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| 3'-nitrotyrosine on Y | — | 5 |
| 3-hydroxyproline on P | UNIMOD:35 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-methacryllysine on K | — | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| N6-lipoyllysine on K | UNIMOD:42 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| N6-malonyllysine on K | — | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| ADP-ribosylation on S | UNIMOD:213 | 1 |
| Allysine on K | UNIMOD:352 | 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 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Lysino-D-alanine (Lys) on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(retinylidene)lysine on K | UNIMOD:380 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-glutathionyl cysteine on C | UNIMOD:55 | 1 |
| S-methylcysteine on C | UNIMOD:34 | 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
2351173d02b25c07, written 2026-10-29T10:21:51+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