Generated summary
PXD014274 is a DDA label-free dataset (Mus musculus) with 38 runs, 38 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 116,639 PSMs, 6,415 peptidoforms and 1,318 protein groups, and the repository holds 7,280 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 5 for information
count_mismatch warning
The bundle holds 6416 where the producer reported 6415 (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 6416 where the producer reported 6415 (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 116639 where the producer reported 116638 (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 116639 where the producer reported 116638 (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
61.81% of protein intensity in the worst file, 22.57% median across 38 files (DEF-QC-9 v3.5)
61.81% of protein intensity in the worst file, 22.57% median across 38 files (DEF-QC-9 v3.5)
low_core_use warning
14.41 avg cores of 32 allowed (S5)
14.41 avg cores of 32 allowed (S5)
occupancy_not_stored warning
Of 40330 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 72 duplicate entry for one site and run (identical values; same protein group); 1709 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 40330 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 72 duplicate entry for one site and run (identical values; same protein group); 1709 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 no row for 6 searched run(s), each given a synthetic sample with no annotation: Lib1, Lib1_2, Lib2, Lib2_2, Lib3, Lib3_2. sdrf_status is `partial`.
The SDRF was used only for the runs it names that were searched: it names no row for 6 searched run(s), each given a synthetic sample with no annotation: Lib1, Lib1_2, Lib2, Lib2_2, Lib3, Lib3_2. 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: disease: Alzheimer disease, normal; organism part: hippocampal formation. 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: disease: Alzheimer disease, normal; organism part: hippocampal formation. 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: 1069 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: 1069 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), 3 row(s) dropped, e.g. PXD014274:D3Z748;F6WRP6;K9J7B2;P70691;Q62452;Q63886;Q64435;Q6ZQM8 written 4 times; quant_values: 38 identifier(s), 114 row(s) dropped, e.g. PXD014274:Lib1:label_free:protein_group:PXD014274:D3Z748;F6WRP6;K9J7B2;P70691;Q62452;Q63886;Q64435;Q6ZQM8:QuantProject:DEF-PROT-SPC written 4 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), 3 row(s) dropped, e.g. PXD014274:D3Z748;F6WRP6;K9J7B2;P70691;Q62452;Q63886;Q64435;Q6ZQM8 written 4 times; quant_values: 38 identifier(s), 114 row(s) dropped, e.g. PXD014274:Lib1:label_free:protein_group:PXD014274:D3Z748;F6WRP6;K9J7B2;P70691;Q62452;Q63886;Q64435;Q6ZQM8:QuantProject:DEF-PROT-SPC written 4 times. The full list is in bundle.json under collapsed_duplicates.
excluded_from_search info
The deposited file Tg1_L_Ctr.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 9aee7c1c25203eea5183b484ac6a34ed598d4c17297061e547bdc6f5c8baeaeb.
The deposited file Tg1_L_Ctr.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 9aee7c1c25203eea5183b484ac6a34ed598d4c17297061e547bdc6f5c8baeaeb.
excluded_from_search info
The deposited file Tg1_R_Ctr.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 799b6a4a8c8a51996b20a4818a3d255751ab52843b75a9122462390cd99ab0db.
The deposited file Tg1_R_Ctr.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 799b6a4a8c8a51996b20a4818a3d255751ab52843b75a9122462390cd99ab0db.
excluded_from_search info
The deposited file Tg2_L.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 6fae6fb43a7a8b199abdabb24fb944077fb5d893b05d5b15b3381f808020b2eb.
The deposited file Tg2_L.raw was left out of the search, so it has no run row, no PSMs and no quantities here. Producer's reason: D52: failed qc_spectra on too_few_ms2 (a blank or failed injection); excluded with a record instead of dropping the deposit. Deposited sha256: 6fae6fb43a7a8b199abdabb24fb944077fb5d893b05d5b15b3381f808020b2eb.
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 | 116,639 |
| Peptidoforms at 1% FDR | 6,415 |
| Protein groups at 1% FDR | 1,318 |
| PTM sites | 7,280 |
| Quantitative values | 261,672 |
| PSMs, all (including decoys and sub-threshold) | 239,892 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 29.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 42.6% |
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
- 38 / 38
- Sample metadata
- partial
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- a086cd029e63
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 1,053 |
| Oxidation on M | UNIMOD:35 | 971 |
| Deamidation on Q | UNIMOD:7 | 883 |
| Deamidation on N | UNIMOD:7 | 799 |
| Citrullination on R | UNIMOD:7 | 259 |
| Hydroxylation on P | UNIMOD:35 | 215 |
| Ammonia loss on N | UNIMOD:385 | 155 |
| Sodium on E | UNIMOD:30 | 135 |
| Hydroxylation on N | UNIMOD:35 | 131 |
| Magnesium on E | UNIMOD:956 | 126 |
| Sodium on D | UNIMOD:30 | 113 |
| Hydroxylation on K | UNIMOD:35 | 86 |
| Magnesium on D | UNIMOD:956 | 86 |
| Calcium on D | UNIMOD:951 | 74 |
| Calcium on E | UNIMOD:951 | 73 |
| Methylation on K | UNIMOD:34 | 69 |
| Carbamyl on X | UNIMOD:5 | 67 |
| Phosphoserine on S | UNIMOD:21 | 57 |
| Carbamyl on M | UNIMOD:5 | 55 |
| Hydroxybutyrylation on K | — | 52 |
| Acetylation on K | UNIMOD:1 | 47 |
| Methylation on R | UNIMOD:34 | 46 |
| Carboxylation on E | UNIMOD:299 | 42 |
| Dimethylation on K | UNIMOD:36 | 42 |
| N-acetylalanine on A | UNIMOD:1 | 41 |
| Carboxylation on D | UNIMOD:299 | 38 |
| Nitrosylation on Y | UNIMOD:354 | 38 |
| Potassium on D | UNIMOD:530 | 31 |
| Carboxylation on K | UNIMOD:299 | 30 |
| Trimethylation on K | UNIMOD:37 | 30 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 28 |
| Carbamyl on R | UNIMOD:5 | 27 |
| Butyrylation on K | UNIMOD:1289 | 26 |
| Acetylation on X | UNIMOD:1 | 25 |
| Dimethylation on R | UNIMOD:36 | 24 |
| Malonylation on K | UNIMOD:747 | 24 |
| Formylation on K | UNIMOD:122 | 22 |
| Carbamyl on K | UNIMOD:5 | 21 |
| Phosphorylation on S | UNIMOD:21 | 21 |
| Potassium on E | UNIMOD:530 | 21 |
| N6-acetyllysine on K | UNIMOD:1 | 18 |
| Ammonia loss on C | UNIMOD:385 | 17 |
| Crotonylation on K | UNIMOD:1363 | 17 |
| Glutarylation on K | UNIMOD:1848 | 15 |
| HexNAc on T | UNIMOD:43 | 15 |
| N-acetylserine on S | UNIMOD:1 | 15 |
| Succinylation on K | UNIMOD:64 | 15 |
| Fe[II] on E | UNIMOD:952 | 11 |
| Phosphorylation on T | UNIMOD:21 | 11 |
| Phosphothreonine on T | UNIMOD:21 | 10 |
| HexNAc on S | UNIMOD:43 | 9 |
| N6-methyllysine on K | UNIMOD:34 | 8 |
| Water Loss on E | UNIMOD:27 | 8 |
| Fe[III] on D | UNIMOD:1870 | 7 |
| Fe[II] on D | UNIMOD:952 | 7 |
| Carbamyl on C | UNIMOD:5 | 6 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| Deamidated asparagine on N | UNIMOD:7 | 4 |
| N-acetylmethionine on M | UNIMOD:1 | 4 |
| N6-succinyllysine on K | — | 4 |
| Nitrosylation on C | UNIMOD:275 | 4 |
| Omega-N-methylarginine on R | UNIMOD:34 | 4 |
| Phosphorylation on Y | UNIMOD:21 | 4 |
| Sulfonation on Y | UNIMOD:40 | 4 |
| Fe[III] on E | UNIMOD:1870 | 3 |
| N-acetylthreonine on T | UNIMOD:1 | 3 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 4-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N-acetylglycine on G | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| Citrulline on R | UNIMOD:7 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-malonyllysine on K | — | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
554d3bb13e935f75, written 2026-10-29T09:24:00+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