Generated summary
PXD044773 is a DDA label-free dataset (Homo sapiens) with 21 runs, 21 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 423,041 PSMs, 33,732 peptidoforms and 3,645 protein groups, and the repository holds 21,783 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
contaminant_label_unresolved warning
21 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: O76009, O76011, O95678, P02768, P08729.
21 protein(s) share a PSM row with proteins of another kind, and the searched databases could not say which they are (not on disk, or in both a target and the contaminant database under TCAmbiguity unknown). Each was given its row's label, contaminant over target, so `is_contaminant` may over-state for them: O76009, O76011, O95678, P02768, P08729.
count_mismatch warning
The bundle holds 423041 where the producer reported 423050 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 423041 where the producer reported 423050 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
high_contamination warning
14.10% of protein intensity in the worst file, 1.35% median across 21 files (DEF-QC-9 v3.5)
14.10% of protein intensity in the worst file, 1.35% median across 21 files (DEF-QC-9 v3.5)
no_design_file warning
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
occupancy_not_stored warning
Of 71487 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 29 segment's accession not determinable from the sequences. '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 71487 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 29 segment's accession not determinable from the sequences. '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_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: glioblastoma; organism part: Subventricular zone. 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: glioblastoma; organism part: Subventricular zone. 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: 4524 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; 67 named a protein the searched databases carry with different sequences, where the search's TCAmbiguity does not say which one it searched (O76011, P19013). 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: 4524 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; 67 named a protein the searched databases carry with different sequences, where the search's TCAmbiguity does not say which one it searched (O76011, P19013). Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.
upstream_provenance_changed warning
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD044773/02_fetch/provenance.json) with sha256 b6c3dc6e40831ed90dc9e00fe05094aa20c4330148bc0db5179577ff00780592, and the file there now has 725845a28b6ba11aeb366247412a07cda0f05e565a786f3d60a08ee8c299896e: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the fetch stage is gone unless the producer archived it.
The search recorded its upstream 'fetch' provenance (run_2026-09-21/PXD044773/02_fetch/provenance.json) with sha256 b6c3dc6e40831ed90dc9e00fe05094aa20c4330148bc0db5179577ff00780592, and the file there now has 725845a28b6ba11aeb366247412a07cda0f05e565a786f3d60a08ee8c299896e: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the fetch stage is gone unless the producer archived it.
no_output_sdrf info
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
occupancy_decoy_groups info
76 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
76 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 | 423,041 |
| Peptidoforms at 1% FDR | 33,732 |
| Protein groups at 1% FDR | 3,645 |
| PTM sites | 21,783 |
| Quantitative values | 424,744 |
| PSMs, all (including decoys and sub-threshold) | 1,100,856 |
| MS2 identification rate (aging:DEF-ID-RATE) | 31.9% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 3.2% |
How it was measured
- Organism searched
- Homo sapiens (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
- 21 / 21
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000005640_AND_revi_2026_09_18_agingPTM-v1.xml
- Pipeline commit
- 19dd466d103f
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 6,255 |
| Oxidation on M | UNIMOD:35 | 5,120 |
| Deamidation on N | UNIMOD:7 | 1,858 |
| Deamidation on Q | UNIMOD:7 | 969 |
| Hydroxylation on P | UNIMOD:35 | 737 |
| Carbamyl on X | UNIMOD:5 | 552 |
| Hydroxylation on N | UNIMOD:35 | 511 |
| Fe[II] on E | UNIMOD:952 | 500 |
| Fe[II] on D | UNIMOD:952 | 499 |
| Fe[III] on E | UNIMOD:1870 | 380 |
| Fe[III] on D | UNIMOD:1870 | 333 |
| Hydroxylation on K | UNIMOD:35 | 301 |
| Ammonia loss on N | UNIMOD:385 | 254 |
| Citrullination on R | UNIMOD:7 | 197 |
| Ammonia loss on C | UNIMOD:385 | 192 |
| N-acetylalanine on A | UNIMOD:1 | 186 |
| Methylation on K | UNIMOD:34 | 156 |
| Methylation on R | UNIMOD:34 | 103 |
| Phosphoserine on S | UNIMOD:21 | 100 |
| Carbamyl on K | UNIMOD:5 | 88 |
| Sodium on D | UNIMOD:30 | 79 |
| Sodium on E | UNIMOD:30 | 77 |
| N-acetylserine on S | UNIMOD:1 | 61 |
| 4-hydroxyproline on P | UNIMOD:35 | 57 |
| N-acetylmethionine on M | UNIMOD:1 | 57 |
| Acetylation on X | UNIMOD:1 | 54 |
| Carbamyl on M | UNIMOD:5 | 54 |
| Calcium on D | UNIMOD:951 | 50 |
| Magnesium on E | UNIMOD:956 | 46 |
| N6-acetyllysine on K | UNIMOD:1 | 45 |
| Calcium on E | UNIMOD:951 | 42 |
| Dimethylation on K | UNIMOD:36 | 41 |
| Magnesium on D | UNIMOD:956 | 38 |
| Acetylation on K | UNIMOD:1 | 35 |
| Carboxylation on E | UNIMOD:299 | 35 |
| Phosphorylation on S | UNIMOD:21 | 32 |
| Water Loss on E | UNIMOD:27 | 31 |
| Dimethylation on R | UNIMOD:36 | 29 |
| Phosphothreonine on T | UNIMOD:21 | 28 |
| Formylation on K | UNIMOD:122 | 26 |
| Carboxylation on D | UNIMOD:299 | 19 |
| Phosphorylation on T | UNIMOD:21 | 19 |
| HexNAc on S | UNIMOD:43 | 16 |
| N-acetylthreonine on T | UNIMOD:1 | 16 |
| Potassium on D | UNIMOD:530 | 16 |
| Carbamyl on R | UNIMOD:5 | 15 |
| Omega-N-methylarginine on R | UNIMOD:34 | 15 |
| Carboxylation on K | UNIMOD:299 | 14 |
| GG (Ubiquitination Site) on K | — | 14 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Potassium on E | UNIMOD:530 | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 12 |
| Trimethylation on K | UNIMOD:37 | 12 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 11 |
| Deamidated asparagine on N | UNIMOD:7 | 10 |
| HexNAc on T | UNIMOD:43 | 10 |
| Carbamyl on C | UNIMOD:5 | 9 |
| Nitrosylation on Y | UNIMOD:354 | 8 |
| Phosphorylation on Y | UNIMOD:21 | 8 |
| Cu[I] on E | UNIMOD:531 | 7 |
| Cu[I] on D | UNIMOD:531 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N-myristoyl glycine on G | UNIMOD:45 | 5 |
| Glutarylation on K | UNIMOD:1848 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 3 |
| Hydroxybutyrylation on K | — | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| N6-malonyllysine on K | — | 2 |
| N6-succinyllysine on K | — | 2 |
| Nitrosylation on C | UNIMOD:275 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| Sulfonation 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
47b17f3926ffe277, written 2026-10-29T10:29:28+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