Generated summary
PXD048877 is a DDA label-free dataset (Mus musculus) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,804,710 PSMs, 49,168 peptidoforms and 4,864 protein groups, and the repository holds 37,379 PTM sites for it. 5 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, 5 warnings and 2 for information
count_mismatch warning
The bundle holds 49168 where the producer reported 49167 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 49168 where the producer reported 49167 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
count_mismatch warning
The bundle holds 1.80471e+06 where the producer reported 1.80506e+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 1.80471e+06 where the producer reported 1.80506e+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.
occupancy_not_stored warning
Of 220090 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 16 duplicate entry for one site and run (identical values; same protein group); 14289 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 220090 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 16 duplicate entry for one site and run (identical values; same protein group); 14289 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).
sdrf_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: heart. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: organism part: heart. Match on it as text; it has not been mapped to a term.
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: 8798 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: 8798 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: 8 identifier(s), 9 row(s) dropped, e.g. PXD048877:A0AAG1GIT8;A0AAG1GJQ8;A0AB53AJB1 written 3 times; quant_values: 240 identifier(s), 270 row(s) dropped, e.g. PXD048877:EX1_12714_ETZ_Agrin_1_1_011220:label_free:protein_group:PXD048877:A0AAG1GIT8;A0AAG1GJQ8;A0AB53AJB1: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: 8 identifier(s), 9 row(s) dropped, e.g. PXD048877:A0AAG1GIT8;A0AAG1GJQ8;A0AB53AJB1 written 3 times; quant_values: 240 identifier(s), 270 row(s) dropped, e.g. PXD048877:EX1_12714_ETZ_Agrin_1_1_011220:label_free:protein_group:PXD048877:A0AAG1GIT8;A0AAG1GJQ8;A0AB53AJB1:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
219 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
219 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 | 1,804,710 |
| Peptidoforms at 1% FDR | 49,168 |
| Protein groups at 1% FDR | 4,864 |
| PTM sites | 37,379 |
| Quantitative values | 1,251,503 |
| PSMs, all (including decoys and sub-threshold) | 3,731,386 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 53.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.9% |
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
- none
- Instrument vendor
- Thermo
- Runs / samples
- 30 / 30
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 4c062e010587
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 10,661 |
| Deamidation on N | UNIMOD:7 | 5,456 |
| Deamidation on Q | UNIMOD:7 | 4,212 |
| Oxidation on M | UNIMOD:35 | 3,793 |
| Hydroxylation on P | UNIMOD:35 | 1,379 |
| Citrullination on R | UNIMOD:7 | 1,259 |
| Ammonia loss on N | UNIMOD:385 | 765 |
| Hydroxylation on N | UNIMOD:35 | 473 |
| Methylation on K | UNIMOD:34 | 468 |
| Hydroxylation on K | UNIMOD:35 | 416 |
| Phosphoserine on S | UNIMOD:21 | 403 |
| Sodium on E | UNIMOD:30 | 343 |
| Fe[III] on E | UNIMOD:1870 | 329 |
| Fe[III] on D | UNIMOD:1870 | 298 |
| Magnesium on E | UNIMOD:956 | 295 |
| Fe[II] on E | UNIMOD:952 | 286 |
| N-acetylalanine on A | UNIMOD:1 | 285 |
| Sodium on D | UNIMOD:30 | 282 |
| Fe[II] on D | UNIMOD:952 | 264 |
| Ammonia loss on C | UNIMOD:385 | 246 |
| Magnesium on D | UNIMOD:956 | 242 |
| Formylation on K | UNIMOD:122 | 238 |
| Carbamyl on X | UNIMOD:5 | 235 |
| Acetylation on X | UNIMOD:1 | 229 |
| Carbamyl on K | UNIMOD:5 | 214 |
| N6-acetyllysine on K | UNIMOD:1 | 205 |
| Acetylation on K | UNIMOD:1 | 195 |
| Phosphorylation on S | UNIMOD:21 | 188 |
| Methylation on R | UNIMOD:34 | 182 |
| Water Loss on E | UNIMOD:27 | 182 |
| Dimethylation on K | UNIMOD:36 | 162 |
| Phosphorylation on T | UNIMOD:21 | 145 |
| N-acetylmethionine on M | UNIMOD:1 | 141 |
| N-acetylserine on S | UNIMOD:1 | 112 |
| Carbamyl on M | UNIMOD:5 | 108 |
| HexNAc on S | UNIMOD:43 | 107 |
| Trimethylation on K | UNIMOD:37 | 101 |
| Crotonylation on K | UNIMOD:1363 | 99 |
| HexNAc on T | UNIMOD:43 | 95 |
| Phosphothreonine on T | UNIMOD:21 | 93 |
| Dimethylation on R | UNIMOD:36 | 91 |
| N6-succinyllysine on K | — | 90 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 76 |
| Calcium on D | UNIMOD:951 | 72 |
| Calcium on E | UNIMOD:951 | 64 |
| Malonylation on K | UNIMOD:747 | 64 |
| 4-hydroxyproline on P | UNIMOD:35 | 63 |
| Carboxylation on E | UNIMOD:299 | 62 |
| Carboxylation on D | UNIMOD:299 | 61 |
| Cu[I] on D | UNIMOD:531 | 61 |
| Glutarylation on K | UNIMOD:1848 | 61 |
| Hydroxybutyrylation on K | — | 53 |
| Omega-N-methylarginine on R | UNIMOD:34 | 53 |
| Succinylation on K | UNIMOD:64 | 52 |
| Nitrosylation on Y | UNIMOD:354 | 44 |
| Potassium on D | UNIMOD:530 | 41 |
| Phosphorylation on Y | UNIMOD:21 | 39 |
| N6-methyllysine on K | UNIMOD:34 | 37 |
| Carboxylation on K | UNIMOD:299 | 36 |
| Butyrylation on K | UNIMOD:1289 | 35 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 34 |
| Nitrosylation on C | UNIMOD:275 | 30 |
| Carbamyl on R | UNIMOD:5 | 28 |
| Sulfonation on Y | UNIMOD:40 | 28 |
| Carbamyl on C | UNIMOD:5 | 25 |
| Cu[I] on E | UNIMOD:531 | 24 |
| N-acetylthreonine on T | UNIMOD:1 | 24 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 23 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 22 |
| Potassium on E | UNIMOD:530 | 22 |
| Phosphotyrosine on Y | UNIMOD:21 | 21 |
| Deamidated asparagine on N | UNIMOD:7 | 18 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 17 |
| N6-glutaryllysine on K | — | 16 |
| N-myristoyl glycine on G | UNIMOD:45 | 13 |
| Zinc on E | UNIMOD:954 | 13 |
| N6-methacryllysine on K | — | 12 |
| Zinc on D | UNIMOD:954 | 12 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 9 |
| Dimethylated arginine on R | UNIMOD:36 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| Citrulline on R | UNIMOD:7 | 6 |
| N6-lipoyllysine on K | UNIMOD:42 | 6 |
| ADP-ribosylation on S | UNIMOD:213 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 5-hydroxylysine on K | UNIMOD:35 | 4 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 4 |
| S-nitrosocysteine on C | UNIMOD:275 | 4 |
| Glu to PyroGlu on Q | UNIMOD:28 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Allysine on K | UNIMOD:352 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N6-crotonyllysine on K | — | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| S-(2,3-dicarboxypropyl)cysteine on C | — | 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
12a0e55ac9184f69, written 2026-10-29T13:19:43+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group