Generated summary
PXD018999 is a DDA label-free dataset (Mus musculus) with 48 runs, 48 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 974,746 PSMs, 78,290 peptidoforms and 8,239 protein groups, and the repository holds 46,440 PTM sites for it. 8 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, 8 warnings and 2 for information
count_mismatch warning
The bundle holds 78291 where the producer reported 78289 (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 78291 where the producer reported 78289 (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 974746 where the producer reported 974990 (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 974746 where the producer reported 974990 (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.
high_contamination warning
5.71% of protein intensity in the worst file, 1.16% median across 48 files (DEF-QC-9 v3.5)
5.71% of protein intensity in the worst file, 1.16% median across 48 files (DEF-QC-9 v3.5)
low_core_use warning
7.89 avg cores of 32 allowed (S5)
7.89 avg cores of 32 allowed (S5)
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 188040 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 15846 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 188040 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 15846 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).
spectral_library warning
mouse's current library moved from version 101 to 102 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD018999\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-25-15-19-36.msp and has NOT been registered, so nothing was lost; merge it deliberately.
mouse's current library moved from version 101 to 102 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD018999\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-25-15-19-36.msp and has NOT been registered, so nothing was lost; merge it deliberately.
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: 3202 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: 3202 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), 1 row(s) dropped, e.g. PXD018999:Q8C0T1;Q9Z2G1 written 2 times; quant_values: 48 identifier(s), 48 row(s) dropped, e.g. PXD018999:mouse_kidney_hypoxic_1_fraction_1_replicate_1:label_free:protein_group:PXD018999:Q8C0T1;Q9Z2G1: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: 1 identifier(s), 1 row(s) dropped, e.g. PXD018999:Q8C0T1;Q9Z2G1 written 2 times; quant_values: 48 identifier(s), 48 row(s) dropped, e.g. PXD018999:mouse_kidney_hypoxic_1_fraction_1_replicate_1:label_free:protein_group:PXD018999:Q8C0T1;Q9Z2G1:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
105 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
105 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 | 974,746 |
| Peptidoforms at 1% FDR | 78,290 |
| Protein groups at 1% FDR | 8,239 |
| PTM sites | 46,440 |
| Quantitative values | 1,595,836 |
| PSMs, all (including decoys and sub-threshold) | 1,895,057 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 72.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.5% |
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
- 48 / 48
- 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 | 18,037 |
| Oxidation on M | UNIMOD:35 | 5,200 |
| Deamidation on N | UNIMOD:7 | 4,767 |
| Deamidation on Q | UNIMOD:7 | 3,062 |
| Ammonia loss on N | UNIMOD:385 | 1,548 |
| Hydroxylation on P | UNIMOD:35 | 1,387 |
| Ammonia loss on C | UNIMOD:385 | 877 |
| Formylation on K | UNIMOD:122 | 815 |
| Methylation on K | UNIMOD:34 | 791 |
| Citrullination on R | UNIMOD:7 | 704 |
| Phosphoserine on S | UNIMOD:21 | 675 |
| Hydroxylation on N | UNIMOD:35 | 567 |
| Phosphorylation on S | UNIMOD:21 | 397 |
| Phosphorylation on T | UNIMOD:21 | 368 |
| Acetylation on X | UNIMOD:1 | 354 |
| Methylation on R | UNIMOD:34 | 342 |
| N-acetylalanine on A | UNIMOD:1 | 336 |
| Carbamyl on M | UNIMOD:5 | 303 |
| Hydroxylation on K | UNIMOD:35 | 287 |
| Carbamyl on X | UNIMOD:5 | 262 |
| Acetylation on K | UNIMOD:1 | 248 |
| Water Loss on E | UNIMOD:27 | 244 |
| Fe[III] on E | UNIMOD:1870 | 230 |
| N-acetylmethionine on M | UNIMOD:1 | 206 |
| Sulfonation on Y | UNIMOD:40 | 193 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 173 |
| Fe[III] on D | UNIMOD:1870 | 161 |
| N6-acetyllysine on K | UNIMOD:1 | 153 |
| Carbamyl on K | UNIMOD:5 | 152 |
| Trimethylation on K | UNIMOD:37 | 151 |
| N-acetylserine on S | UNIMOD:1 | 139 |
| Dimethylation on K | UNIMOD:36 | 134 |
| Phosphothreonine on T | UNIMOD:21 | 134 |
| Sodium on D | UNIMOD:30 | 116 |
| Sodium on E | UNIMOD:30 | 111 |
| Phosphorylation on Y | UNIMOD:21 | 83 |
| HexNAc on S | UNIMOD:43 | 77 |
| Magnesium on E | UNIMOD:956 | 77 |
| Carboxylation on D | UNIMOD:299 | 76 |
| Carboxylation on E | UNIMOD:299 | 75 |
| Glutarylation on K | UNIMOD:1848 | 75 |
| Magnesium on D | UNIMOD:956 | 74 |
| Dimethylation on R | UNIMOD:36 | 73 |
| Butyrylation on K | UNIMOD:1289 | 67 |
| Omega-N-methylarginine on R | UNIMOD:34 | 66 |
| Carbamyl on C | UNIMOD:5 | 65 |
| Fe[II] on E | UNIMOD:952 | 63 |
| HexNAc on T | UNIMOD:43 | 61 |
| 4-hydroxyproline on P | UNIMOD:35 | 55 |
| Fe[II] on D | UNIMOD:952 | 52 |
| Calcium on E | UNIMOD:951 | 50 |
| Crotonylation on K | UNIMOD:1363 | 50 |
| Malonylation on K | UNIMOD:747 | 48 |
| Carbamyl on R | UNIMOD:5 | 47 |
| Hydroxybutyrylation on K | — | 47 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 38 |
| N6-succinyllysine on K | — | 36 |
| Nitrosylation on C | UNIMOD:275 | 34 |
| Phosphotyrosine on Y | UNIMOD:21 | 32 |
| N6-glutaryllysine on K | — | 31 |
| Calcium on D | UNIMOD:951 | 28 |
| N6-crotonyllysine on K | — | 28 |
| Carboxylation on K | UNIMOD:299 | 27 |
| N6-methyllysine on K | UNIMOD:34 | 27 |
| Nitrosylation on Y | UNIMOD:354 | 27 |
| N-acetylthreonine on T | UNIMOD:1 | 25 |
| Succinylation on K | UNIMOD:64 | 21 |
| N5-methylglutamine on Q | UNIMOD:34 | 18 |
| N6-methacryllysine on K | — | 18 |
| Potassium on D | UNIMOD:530 | 18 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 16 |
| Potassium on E | UNIMOD:530 | 16 |
| N-myristoyl glycine on G | UNIMOD:45 | 15 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 12 |
| ADP-ribosylation on S | UNIMOD:213 | 11 |
| Cu[I] on D | UNIMOD:531 | 11 |
| Cu[I] on E | UNIMOD:531 | 11 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 10 |
| Zinc on E | UNIMOD:954 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 9 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 9 |
| Pyridoxal phosphate on K | UNIMOD:46 | 8 |
| N6-butyryllysine on K | UNIMOD:1289 | 7 |
| Citrulline on R | UNIMOD:7 | 6 |
| Dimethylated arginine on R | UNIMOD:36 | 5 |
| Glu to PyroGlu on Q | UNIMOD:28 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-propionyllysine on K | UNIMOD:58 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N6-malonyllysine on K | — | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 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 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-methylcysteine on C | UNIMOD:34 | 1 |
| Sulfocysteine on C | UNIMOD:40 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
151af8dac684a432, written 2026-10-29T11:59:50+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