Generated summary
PXD045861 is a DDA label-free dataset (Homo sapiens) with 20 runs, 1 sample and enrichment: proximity_labelling. It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 312,904 PSMs, 10,572 peptidoforms and 2,682 protein groups, and the repository holds 10,588 PTM sites for it. 9 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, 9 warnings and 1 for information
count_mismatch warning
The bundle holds 312904 where the producer reported 312908 (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 312904 where the producer reported 312908 (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
14.78% of protein intensity in the worst file, 9.78% median across 20 files (DEF-QC-9 v3.5)
14.78% of protein intensity in the worst file, 9.78% median across 20 files (DEF-QC-9 v3.5)
low_core_use warning
9.44 avg cores of 32 allowed (S5)
9.44 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 312908/2223625 = 14.07% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 312908/2223625 = 14.07% of MS2 identified (S3)
occupancy_not_stored warning
Of 18221 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4398 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 18221 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4398 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).
peptide_rows_localization_ambiguous warning
10 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 65 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AFADALEVIPMALSENSGM[Common Variable:Oxidation on M]NPIQTM[Common Variable:Oxidation on M]TEVR|AFADALEVIPM[Common Variable:Oxidation on M]ALSENSGMNPIQTM[Common Variable:Oxidation on M]TEVR`, `DAAAIC[Common Fixed:Carbamidomethyl on C]QPSAGVHIVMPGYYSPESM[Common Variable:Oxidation on M]GLLDPATSDGR|DAAAIC[Common Fixed:Carbamidomethyl on C]QPSAGVHIVM[Common Variable:Oxidation on M]PGYYSPESMGLLDPATSDGR`, `DGKDYIFEVMDC[Common Fixed:Carbamidomethyl on C]SM[Common Variable:Oxidation on M]PLIGEHQVEDR|DGKDYIFEVM[Common Variable:Oxidation on M]DC[Common Fixed:Carbamidomethyl on C]SMPLIGEHQVEDR`.
10 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 65 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AFADALEVIPMALSENSGM[Common Variable:Oxidation on M]NPIQTM[Common Variable:Oxidation on M]TEVR|AFADALEVIPM[Common Variable:Oxidation on M]ALSENSGMNPIQTM[Common Variable:Oxidation on M]TEVR`, `DAAAIC[Common Fixed:Carbamidomethyl on C]QPSAGVHIVMPGYYSPESM[Common Variable:Oxidation on M]GLLDPATSDGR|DAAAIC[Common Fixed:Carbamidomethyl on C]QPSAGVHIVM[Common Variable:Oxidation on M]PGYYSPESMGLLDPATSDGR`, `DGKDYIFEVMDC[Common Fixed:Carbamidomethyl on C]SM[Common Variable:Oxidation on M]PLIGEHQVEDR|DGKDYIFEVM[Common Variable:Oxidation on M]DC[Common Fixed:Carbamidomethyl on C]SMPLIGEHQVEDR`.
sdrf_partial warning
The SDRF was used only for the runs it names that were searched: it names 25 file(s) the search did not use, whose rows were not used: QEp21-2495_Cai_AD-201_NoAb, QEp21-2499_Cai_AD-203_NoAb, QEp21-2503_Cai_AD-205_NoAb, QEp21-2508_Cai_AD-201_Caspr, QEp21-2512_Cai_AD-203_Caspr, QEp21-2516_Cai_AD-205_Caspr, QEp21-2521_Cai_WT-200_Caspr, QEp21-2525_Cai_WT-202_Caspr, QEp21-2529_Cai_WT-204_Caspr, QEp21-3981_Cai_AD400192-noAb .... sdrf_status is `partial`.
The SDRF was used only for the runs it names that were searched: it names 25 file(s) the search did not use, whose rows were not used: QEp21-2495_Cai_AD-201_NoAb, QEp21-2499_Cai_AD-203_NoAb, QEp21-2503_Cai_AD-205_NoAb, QEp21-2508_Cai_AD-201_Caspr, QEp21-2512_Cai_AD-203_Caspr, QEp21-2516_Cai_AD-205_Caspr, QEp21-2521_Cai_WT-200_Caspr, QEp21-2525_Cai_WT-202_Caspr, QEp21-2529_Cai_WT-204_Caspr, QEp21-3981_Cai_AD400192-noAb .... sdrf_status is `partial`.
sdrf_skeleton warning
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
The deposited SDRF carries no biological annotation: organism part, cell type, disease and individual are all absent. Sample-level questions cannot be answered for this dataset until it is curated.
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: 878 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: 878 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.
occupancy_decoy_groups info
631 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
631 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 | 312,904 |
| Peptidoforms at 1% FDR | 10,572 |
| Protein groups at 1% FDR | 2,682 |
| PTM sites | 10,588 |
| Quantitative values | 381,904 |
| PSMs, all (including decoys and sub-threshold) | 4,523,340 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 14.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.9% |
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
- proximity_labelling
- Instrument vendor
- Thermo
- Runs / samples
- 20 / 1
- Sample metadata
- partial
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 5,745 |
| Carbamidomethyl on C | UNIMOD:4 | 3,344 |
| Hydroxylation on P | UNIMOD:35 | 218 |
| Phosphoserine on S | UNIMOD:21 | 216 |
| N-acetylalanine on A | UNIMOD:1 | 154 |
| Phosphorylation on S | UNIMOD:21 | 152 |
| Phosphorylation on T | UNIMOD:21 | 88 |
| N-acetylserine on S | UNIMOD:1 | 62 |
| 4-hydroxyproline on P | UNIMOD:35 | 55 |
| N-acetylmethionine on M | UNIMOD:1 | 55 |
| Phosphothreonine on T | UNIMOD:21 | 46 |
| Acetylation on X | UNIMOD:1 | 44 |
| N6-acetyllysine on K | UNIMOD:1 | 33 |
| Omega-N-methylarginine on R | UNIMOD:34 | 31 |
| Methylation on K | UNIMOD:34 | 29 |
| Hydroxylation on K | UNIMOD:35 | 26 |
| N6-succinyllysine on K | — | 22 |
| N-acetylthreonine on T | UNIMOD:1 | 15 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 14 |
| HexNAc on S | UNIMOD:43 | 13 |
| Malonylation on K | UNIMOD:747 | 13 |
| Citrulline on R | UNIMOD:7 | 11 |
| HexNAc on T | UNIMOD:43 | 11 |
| Phosphorylation on Y | UNIMOD:21 | 10 |
| Deamidated asparagine on N | UNIMOD:7 | 8 |
| Dimethylation on K | UNIMOD:36 | 8 |
| Acetylation on K | UNIMOD:1 | 7 |
| Hydroxyproline on P | UNIMOD:35 | 7 |
| Methylation on R | UNIMOD:34 | 7 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Dimethylation on R | UNIMOD:36 | 5 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 4 |
| N6-crotonyllysine on K | — | 4 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-benzoyllysine on K | UNIMOD:136 | 3 |
| Succinylation on K | UNIMOD:64 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Deamidated glutamine on Q | UNIMOD:7 | 2 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-methyllysine on K | UNIMOD:34 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| Tele-methylhistidine on H | UNIMOD:34 | 2 |
| Trimethylation on K | UNIMOD:37 | 2 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| Butyrylation on K | UNIMOD:1289 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Glutarylation on K | UNIMOD:1848 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
377c9f3a53bfca01, written 2026-10-29T18:24:14+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