Generated summary
PXD034590 is a DDA label-free dataset (Mus musculus) with 81 runs, 81 samples and enrichment: affinity_purification. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 2,574,920 PSMs, 90,744 peptidoforms and 6,467 protein groups, and the repository holds 43,185 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
count_mismatch warning
The bundle holds 2.57492e+06 where the producer reported 2.57523e+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 2.57492e+06 where the producer reported 2.57523e+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.
high_contamination warning
79.13% of protein intensity in the worst file, 1.25% median across 81 files (DEF-QC-9 v3.5)
79.13% of protein intensity in the worst file, 1.25% median across 81 files (DEF-QC-9 v3.5)
occupancy_not_stored warning
Of 214945 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7 segment's accession not determinable from the sequences; 21690 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 214945 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7 segment's accession not determinable from the sequences; 21690 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_partial warning
The SDRF was used only for the runs it names that were searched: it names 24 file(s) the search did not use, whose rows were not used: 20210929_DS_Col99B_ATG5KO_Thirdtime_1_1, 20210929_DS_Col99B_ATG5KO_Thirdtime_1_2, 20210929_DS_Col99B_ATG5KO_Thirdtime_1_3, 20210929_DS_Col99B_ATG5KO_Thirdtime_2_4, 20210929_DS_Col99B_ATG5KO_Thirdtime_2_5, 20210929_DS_Col99B_ATG5KO_Thirdtime_2_6, 20210929_DS_Col99B_ATG5KO_Thirdtime_3_7, 20210929_DS_Col99B_ATG5KO_Thirdtime_3_8, 20210929_DS_Col99B_ATG5KO_Thirdtime_3_9, 20210929_DS_Col99B_ATG5KO_Thirdtime_4_10 .... sdrf_status is `partial`.
The SDRF was used only for the runs it names that were searched: it names 24 file(s) the search did not use, whose rows were not used: 20210929_DS_Col99B_ATG5KO_Thirdtime_1_1, 20210929_DS_Col99B_ATG5KO_Thirdtime_1_2, 20210929_DS_Col99B_ATG5KO_Thirdtime_1_3, 20210929_DS_Col99B_ATG5KO_Thirdtime_2_4, 20210929_DS_Col99B_ATG5KO_Thirdtime_2_5, 20210929_DS_Col99B_ATG5KO_Thirdtime_2_6, 20210929_DS_Col99B_ATG5KO_Thirdtime_3_7, 20210929_DS_Col99B_ATG5KO_Thirdtime_3_8, 20210929_DS_Col99B_ATG5KO_Thirdtime_3_9, 20210929_DS_Col99B_ATG5KO_Thirdtime_4_10 .... sdrf_status is `partial`.
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: brain. 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: brain. 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: 5862 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: 5862 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: 12 identifier(s), 30 row(s) dropped, e.g. PXD034590:A0A0B4J1F3;F8VQ94;P97484 written 2 times; quant_values: 972 identifier(s), 2430 row(s) dropped, e.g. PXD034590:202100606_DS_Col099A_AVWP__Aged_A__19:label_free:protein_group:PXD034590:A0A0B4J1F3;F8VQ94;P97484: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: 12 identifier(s), 30 row(s) dropped, e.g. PXD034590:A0A0B4J1F3;F8VQ94;P97484 written 2 times; quant_values: 972 identifier(s), 2430 row(s) dropped, e.g. PXD034590:202100606_DS_Col099A_AVWP__Aged_A__19:label_free:protein_group:PXD034590:A0A0B4J1F3;F8VQ94;P97484:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
49 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
49 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 | 2,574,920 |
| Peptidoforms at 1% FDR | 90,744 |
| Protein groups at 1% FDR | 6,467 |
| PTM sites | 43,185 |
| Quantitative values | 2,331,825 |
| PSMs, all (including decoys and sub-threshold) | 5,285,800 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 66.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.8% |
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
- affinity_purification
- Instrument vendor
- Thermo
- Runs / samples
- 81 / 81
- Sample metadata
- partial
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v5.xml
- Pipeline commit
- ebbdeae0796f
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 14,778 |
| Oxidation on M | UNIMOD:35 | 12,033 |
| Deamidation on N | UNIMOD:7 | 2,915 |
| Sodium on E | UNIMOD:30 | 1,107 |
| Deamidation on Q | UNIMOD:7 | 1,102 |
| Sodium on D | UNIMOD:30 | 894 |
| Phosphoserine on S | UNIMOD:21 | 807 |
| Acetylation on K | UNIMOD:1 | 634 |
| Carbamyl on X | UNIMOD:5 | 571 |
| Acetylation on X | UNIMOD:1 | 512 |
| Ammonia loss on N | UNIMOD:385 | 497 |
| Calcium on E | UNIMOD:951 | 422 |
| Calcium on D | UNIMOD:951 | 383 |
| N-acetylalanine on A | UNIMOD:1 | 379 |
| Fe[III] on E | UNIMOD:1870 | 328 |
| Dimethylation on K | UNIMOD:36 | 317 |
| Ammonia loss on C | UNIMOD:385 | 305 |
| N6-acetyllysine on K | UNIMOD:1 | 285 |
| Magnesium on E | UNIMOD:956 | 274 |
| Hydroxylation on P | UNIMOD:35 | 264 |
| Citrullination on R | UNIMOD:7 | 260 |
| Fe[III] on D | UNIMOD:1870 | 243 |
| Magnesium on D | UNIMOD:956 | 236 |
| Water Loss on E | UNIMOD:27 | 224 |
| Dimethylation on R | UNIMOD:36 | 218 |
| Phosphorylation on S | UNIMOD:21 | 187 |
| Hydroxylation on N | UNIMOD:35 | 184 |
| N-acetylmethionine on M | UNIMOD:1 | 172 |
| Methylation on K | UNIMOD:34 | 151 |
| N-acetylserine on S | UNIMOD:1 | 139 |
| Phosphorylation on T | UNIMOD:21 | 136 |
| Fe[II] on E | UNIMOD:952 | 129 |
| Phosphothreonine on T | UNIMOD:21 | 121 |
| Fe[II] on D | UNIMOD:952 | 117 |
| Potassium on D | UNIMOD:530 | 111 |
| Potassium on E | UNIMOD:530 | 102 |
| HexNAc on S | UNIMOD:43 | 79 |
| Methylation on R | UNIMOD:34 | 79 |
| N6-succinyllysine on K | — | 74 |
| HexNAc on T | UNIMOD:43 | 67 |
| Hydroxylation on K | UNIMOD:35 | 60 |
| Omega-N-methylarginine on R | UNIMOD:34 | 52 |
| Carbamyl on M | UNIMOD:5 | 49 |
| 4-hydroxyproline on P | UNIMOD:35 | 45 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 36 |
| Malonylation on K | UNIMOD:747 | 32 |
| N-acetylthreonine on T | UNIMOD:1 | 32 |
| Trimethylation on K | UNIMOD:37 | 32 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 30 |
| Carbamyl on K | UNIMOD:5 | 28 |
| Crotonylation on K | UNIMOD:1363 | 22 |
| Glutarylation on K | UNIMOD:1848 | 21 |
| Carboxylation on E | UNIMOD:299 | 20 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 20 |
| Formylation on K | UNIMOD:122 | 19 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 17 |
| Succinylation on K | UNIMOD:64 | 17 |
| Phosphotyrosine on Y | UNIMOD:21 | 14 |
| Deamidated asparagine on N | UNIMOD:7 | 13 |
| Hydroxybutyrylation on K | — | 12 |
| Phosphorylation on Y | UNIMOD:21 | 12 |
| Butyrylation on K | UNIMOD:1289 | 10 |
| Carboxylation on D | UNIMOD:299 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 10 |
| N-myristoyl glycine on G | UNIMOD:45 | 10 |
| N6-methyllysine on K | UNIMOD:34 | 10 |
| Carboxylation on K | UNIMOD:299 | 9 |
| Carbamyl on C | UNIMOD:5 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 7 |
| N6-glutaryllysine on K | — | 6 |
| Citrulline on R | UNIMOD:7 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 5 |
| N6-crotonyllysine on K | — | 5 |
| (3S)-3-hydroxyasparagine on N | — | 4 |
| 3'-nitrotyrosine on Y | — | 4 |
| Carbamyl on R | UNIMOD:5 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N6-methacryllysine on K | — | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| N6-malonyllysine on K | — | 2 |
| Propionamide on C | — | 2 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Cu[I] on D | UNIMOD:531 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphthamide on H | UNIMOD:375 | 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-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-lipoyllysine on K | UNIMOD:42 | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Sulfocysteine on C | UNIMOD:40 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| Zinc on E | UNIMOD:954 | 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
0f4c6af19fa68ab7, written 2026-10-29T11:10:04+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