Generated summary
PXD043001 is a DDA label-free dataset (Mus musculus) with 40 runs, 40 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,821,853 PSMs, 75,455 peptidoforms and 8,548 protein groups, and the repository holds 60,348 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 2.82185e+06 where the producer reported 2.82437e+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 2.82185e+06 where the producer reported 2.82437e+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 266714 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 40 duplicate entry for one site and run (identical values; same protein group); 11918 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 266714 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 40 duplicate entry for one site and run (identical values; same protein group); 11918 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: 11154 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: 11154 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: 17 identifier(s), 20 row(s) dropped, e.g. PXD043001:A0A088MLT8;P0DPB4 written 2 times; quant_values: 680 identifier(s), 800 row(s) dropped, e.g. PXD043001:Ecl1_0121_R0032-01_S001436_L_H01_LFQ_01:label_free:protein_group:PXD043001:A0A088MLT8;P0DPB4: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: 17 identifier(s), 20 row(s) dropped, e.g. PXD043001:A0A088MLT8;P0DPB4 written 2 times; quant_values: 680 identifier(s), 800 row(s) dropped, e.g. PXD043001:Ecl1_0121_R0032-01_S001436_L_H01_LFQ_01:label_free:protein_group:PXD043001:A0A088MLT8;P0DPB4:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
266 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
266 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 | 2,821,853 |
| Peptidoforms at 1% FDR | 75,455 |
| Protein groups at 1% FDR | 8,548 |
| PTM sites | 60,348 |
| Quantitative values | 1,479,469 |
| PSMs, all (including decoys and sub-threshold) | 5,843,307 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 66.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.0% |
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
- 40 / 40
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0ba5e4c3fd33
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 16,699 |
| Oxidation on M | UNIMOD:35 | 10,062 |
| Deamidation on N | UNIMOD:7 | 7,863 |
| Deamidation on Q | UNIMOD:7 | 7,419 |
| Hydroxylation on P | UNIMOD:35 | 2,296 |
| Citrullination on R | UNIMOD:7 | 2,289 |
| Hydroxylation on N | UNIMOD:35 | 1,178 |
| Fe[III] on E | UNIMOD:1870 | 1,035 |
| Fe[III] on D | UNIMOD:1870 | 852 |
| Phosphoserine on S | UNIMOD:21 | 759 |
| Ammonia loss on N | UNIMOD:385 | 703 |
| Hydroxylation on K | UNIMOD:35 | 656 |
| Fe[II] on E | UNIMOD:952 | 541 |
| Water Loss on E | UNIMOD:27 | 466 |
| Fe[II] on D | UNIMOD:952 | 457 |
| Carbamyl on X | UNIMOD:5 | 440 |
| Phosphorylation on S | UNIMOD:21 | 283 |
| Formylation on K | UNIMOD:122 | 280 |
| Methylation on K | UNIMOD:34 | 277 |
| N-acetylalanine on A | UNIMOD:1 | 259 |
| Ammonia loss on C | UNIMOD:385 | 252 |
| Acetylation on K | UNIMOD:1 | 240 |
| Acetylation on X | UNIMOD:1 | 238 |
| Nitrosylation on Y | UNIMOD:354 | 219 |
| N6-acetyllysine on K | UNIMOD:1 | 214 |
| Phosphorylation on T | UNIMOD:21 | 209 |
| Carbamyl on M | UNIMOD:5 | 140 |
| Phosphothreonine on T | UNIMOD:21 | 127 |
| N-acetylserine on S | UNIMOD:1 | 124 |
| N-acetylmethionine on M | UNIMOD:1 | 118 |
| Dimethylation on K | UNIMOD:36 | 114 |
| Methylation on R | UNIMOD:34 | 110 |
| Sodium on E | UNIMOD:30 | 109 |
| Magnesium on E | UNIMOD:956 | 107 |
| Sodium on D | UNIMOD:30 | 100 |
| Carbamyl on K | UNIMOD:5 | 97 |
| Carboxylation on E | UNIMOD:299 | 96 |
| Magnesium on D | UNIMOD:956 | 94 |
| Trimethylation on K | UNIMOD:37 | 93 |
| 4-hydroxyproline on P | UNIMOD:35 | 92 |
| Carboxylation on D | UNIMOD:299 | 87 |
| Crotonylation on K | UNIMOD:1363 | 80 |
| Dimethylation on R | UNIMOD:36 | 76 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 75 |
| Omega-N-methylarginine on R | UNIMOD:34 | 63 |
| Calcium on E | UNIMOD:951 | 60 |
| HexNAc on S | UNIMOD:43 | 57 |
| HexNAc on T | UNIMOD:43 | 56 |
| Calcium on D | UNIMOD:951 | 54 |
| Butyrylation on K | UNIMOD:1289 | 44 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 40 |
| Glutarylation on K | UNIMOD:1848 | 40 |
| N6-succinyllysine on K | — | 39 |
| Phosphorylation on Y | UNIMOD:21 | 38 |
| Potassium on E | UNIMOD:530 | 37 |
| Sulfonation on Y | UNIMOD:40 | 37 |
| Malonylation on K | UNIMOD:747 | 33 |
| Carbamyl on C | UNIMOD:5 | 32 |
| N6-methyllysine on K | UNIMOD:34 | 31 |
| Carbamyl on R | UNIMOD:5 | 30 |
| Nitrosylation on C | UNIMOD:275 | 29 |
| Potassium on D | UNIMOD:530 | 28 |
| Pyridoxal phosphate on K | UNIMOD:46 | 28 |
| Hydroxybutyrylation on K | — | 26 |
| N-acetylthreonine on T | UNIMOD:1 | 24 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 20 |
| Carboxylation on K | UNIMOD:299 | 19 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 19 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 19 |
| Deamidated asparagine on N | UNIMOD:7 | 18 |
| Succinylation on K | UNIMOD:64 | 18 |
| Cu[I] on D | UNIMOD:531 | 17 |
| N-myristoyl glycine on G | UNIMOD:45 | 15 |
| N6-glutaryllysine on K | — | 14 |
| Phosphotyrosine on Y | UNIMOD:21 | 14 |
| 5-hydroxylysine on K | UNIMOD:35 | 13 |
| ADP-ribosylation on S | UNIMOD:213 | 13 |
| Cu[I] on E | UNIMOD:531 | 10 |
| Dimethylated arginine on R | UNIMOD:36 | 10 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 10 |
| Zinc on D | UNIMOD:954 | 9 |
| N-acetylvaline on V | UNIMOD:1 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| Citrulline on R | UNIMOD:7 | 6 |
| Glu to PyroGlu on Q | UNIMOD:28 | 6 |
| N-acetylcysteine on C | UNIMOD:1 | 6 |
| N5-methylglutamine on Q | UNIMOD:34 | 5 |
| N6-methacryllysine on K | — | 5 |
| S-nitrosocysteine on C | UNIMOD:275 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| 3'-nitrotyrosine on Y | — | 4 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 4 |
| N6-benzoyllysine on K | UNIMOD:136 | 4 |
| N6-malonyllysine on K | — | 3 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| Zinc on E | UNIMOD:954 | 3 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| N6-crotonyllysine on K | — | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfenic acid (-SOH) on C | UNIMOD:35 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| O-palmitoyl serine on S | UNIMOD:47 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Sulfotyrosine on Y | UNIMOD:40 | 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
583f589cee2a0ce8, written 2026-10-29T10:46:26+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