Generated summary
PXD039172 is a DDA label-free dataset (Mus musculus) with 98 runs, 98 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,033,275 PSMs, 57,636 peptidoforms and 6,671 protein groups, and the repository holds 41,458 PTM sites for it. 6 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, 6 warnings and 2 for information
calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)
GPTMD/search ran on uncalibrated spectra (S7)
count_mismatch warning
The bundle holds 1.03328e+06 where the producer reported 1.03334e+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 1.03328e+06 where the producer reported 1.03334e+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.
low_core_use warning
15.14 avg cores of 32 allowed (S5)
15.14 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 276761 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12 duplicate entry for one site and run (identical values; same protein group); 50409 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 276761 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12 duplicate entry for one site and run (identical values; same protein group); 50409 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: 2264 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: 2264 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: 3 identifier(s), 5 row(s) dropped, e.g. PXD039172:D3YY49;F6RR30;F8WIQ8 written 2 times; quant_values: 294 identifier(s), 490 row(s) dropped, e.g. PXD039172:P18_008_Parkin_B_KO1:label_free:protein_group:PXD039172:D3YY49;F6RR30;F8WIQ8: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: 3 identifier(s), 5 row(s) dropped, e.g. PXD039172:D3YY49;F6RR30;F8WIQ8 written 2 times; quant_values: 294 identifier(s), 490 row(s) dropped, e.g. PXD039172:P18_008_Parkin_B_KO1:label_free:protein_group:PXD039172:D3YY49;F6RR30;F8WIQ8:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
99 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
99 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 | 1,033,275 |
| Peptidoforms at 1% FDR | 57,636 |
| Protein groups at 1% FDR | 6,671 |
| PTM sites | 41,458 |
| Quantitative values | 1,998,525 |
| PSMs, all (including decoys and sub-threshold) | 1,706,534 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 44.2% |
| 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
- 98 / 98
- 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 |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 10,592 |
| Carbamidomethyl on C | UNIMOD:4 | 7,136 |
| Deamidation on Q | UNIMOD:7 | 3,352 |
| Deamidation on N | UNIMOD:7 | 3,155 |
| Hydroxylation on P | UNIMOD:35 | 2,225 |
| Phosphoserine on S | UNIMOD:21 | 1,226 |
| Hydroxylation on N | UNIMOD:35 | 955 |
| Ammonia loss on N | UNIMOD:385 | 862 |
| Acetylation on X | UNIMOD:1 | 721 |
| Sodium on E | UNIMOD:30 | 681 |
| Phosphorylation on S | UNIMOD:21 | 645 |
| Carbamyl on X | UNIMOD:5 | 634 |
| Sodium on D | UNIMOD:30 | 622 |
| Citrullination on R | UNIMOD:7 | 615 |
| Hydroxylation on K | UNIMOD:35 | 557 |
| N-acetylalanine on A | UNIMOD:1 | 498 |
| Ammonia loss on C | UNIMOD:385 | 497 |
| Formylation on K | UNIMOD:122 | 490 |
| Phosphorylation on T | UNIMOD:21 | 384 |
| Fe[III] on E | UNIMOD:1870 | 364 |
| Fe[III] on D | UNIMOD:1870 | 340 |
| Magnesium on E | UNIMOD:956 | 298 |
| Water Loss on E | UNIMOD:27 | 285 |
| N-acetylmethionine on M | UNIMOD:1 | 284 |
| Fe[II] on E | UNIMOD:952 | 272 |
| Magnesium on D | UNIMOD:956 | 265 |
| Calcium on D | UNIMOD:951 | 256 |
| Fe[II] on D | UNIMOD:952 | 251 |
| Calcium on E | UNIMOD:951 | 240 |
| Methylation on K | UNIMOD:34 | 223 |
| N-acetylserine on S | UNIMOD:1 | 203 |
| Phosphothreonine on T | UNIMOD:21 | 193 |
| Potassium on E | UNIMOD:530 | 122 |
| HexNAc on S | UNIMOD:43 | 120 |
| N6-acetyllysine on K | UNIMOD:1 | 114 |
| HexNAc on T | UNIMOD:43 | 113 |
| Potassium on D | UNIMOD:530 | 113 |
| Acetylation on K | UNIMOD:1 | 109 |
| Carboxylation on D | UNIMOD:299 | 98 |
| Dimethylation on K | UNIMOD:36 | 96 |
| Carboxylation on E | UNIMOD:299 | 90 |
| Methylation on R | UNIMOD:34 | 81 |
| Sulfonation on Y | UNIMOD:40 | 59 |
| 4-hydroxyproline on P | UNIMOD:35 | 56 |
| Carbamyl on K | UNIMOD:5 | 52 |
| Carbamyl on M | UNIMOD:5 | 51 |
| Phosphorylation on Y | UNIMOD:21 | 45 |
| N-acetylthreonine on T | UNIMOD:1 | 44 |
| Dimethylation on R | UNIMOD:36 | 39 |
| Carbamyl on R | UNIMOD:5 | 34 |
| Nitrosylation on C | UNIMOD:275 | 28 |
| Carboxylation on K | UNIMOD:299 | 27 |
| N6-succinyllysine on K | — | 27 |
| Trimethylation on K | UNIMOD:37 | 21 |
| Hydroxybutyrylation on K | — | 20 |
| Omega-N-methylarginine on R | UNIMOD:34 | 18 |
| N5-methylglutamine on Q | UNIMOD:34 | 17 |
| Butyrylation on K | UNIMOD:1289 | 15 |
| Carbamyl on C | UNIMOD:5 | 14 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 14 |
| Phosphotyrosine on Y | UNIMOD:21 | 14 |
| Crotonylation on K | UNIMOD:1363 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 13 |
| Malonylation on K | UNIMOD:747 | 13 |
| Nitrosylation on Y | UNIMOD:354 | 13 |
| Glutarylation on K | UNIMOD:1848 | 12 |
| N-acetylglycine on G | UNIMOD:1 | 10 |
| N-acetylvaline on V | UNIMOD:1 | 10 |
| Cu[I] on D | UNIMOD:531 | 9 |
| Zinc on D | UNIMOD:954 | 8 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 7 |
| Cu[I] on E | UNIMOD:531 | 7 |
| Pyridoxal phosphate on K | UNIMOD:46 | 7 |
| N-acetylcysteine on C | UNIMOD:1 | 6 |
| Succinylation on K | UNIMOD:64 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 5 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 4 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| Glu to PyroGlu on Q | UNIMOD:28 | 4 |
| N6-malonyllysine on K | — | 4 |
| N6-methacryllysine on K | — | 4 |
| Zinc on E | UNIMOD:954 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| N6-methyllysine on K | UNIMOD:34 | 3 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| N6-crotonyllysine on K | — | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine sulfenic acid (-SOH) on C | UNIMOD:35 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 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 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
9907759b57189b7a, written 2026-10-29T12:12:55+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