Generated summary
PXD045887 is a DDA label-free dataset (Homo sapiens) with 40 runs, 40 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 416,021 PSMs, 6,300 peptidoforms and 1,164 protein groups, and the repository holds 6,098 PTM sites for it. 5 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, 5 warnings and 2 for information
low_core_use warning
13.63 avg cores of 32 allowed (S5)
13.63 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: 416021/3336265 = 12.47% 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: 416021/3336265 = 12.47% of MS2 identified (S3)
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 25803 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2646 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 25803 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2646 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: 1080 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: 1080 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: 2 identifier(s), 4 row(s) dropped, e.g. PXD045887:A0AAG2SXN7;O43272 written 2 times; quant_values: 80 identifier(s), 160 row(s) dropped, e.g. PXD045887:280823_Amanda_Vichy_07_1:label_free:protein_group:PXD045887:A0AAG2SXN7;O43272: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: 2 identifier(s), 4 row(s) dropped, e.g. PXD045887:A0AAG2SXN7;O43272 written 2 times; quant_values: 80 identifier(s), 160 row(s) dropped, e.g. PXD045887:280823_Amanda_Vichy_07_1:label_free:protein_group:PXD045887:A0AAG2SXN7;O43272:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
91 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
91 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 | 416,021 |
| Peptidoforms at 1% FDR | 6,300 |
| Protein groups at 1% FDR | 1,164 |
| PTM sites | 6,098 |
| Quantitative values | 294,660 |
| PSMs, all (including decoys and sub-threshold) | 683,284 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 12.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.4% |
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
- not recorded
- Runs / samples
- 40 / 40
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- a086cd029e63
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 2,779 |
| Oxidation on M | UNIMOD:35 | 570 |
| Deamidation on N | UNIMOD:7 | 389 |
| Deamidation on Q | UNIMOD:7 | 352 |
| Citrullination on R | UNIMOD:7 | 165 |
| Ammonia loss on N | UNIMOD:385 | 157 |
| Ammonia loss on C | UNIMOD:385 | 130 |
| Carbamyl on X | UNIMOD:5 | 95 |
| Hydroxylation on P | UNIMOD:35 | 71 |
| N-acetylalanine on A | UNIMOD:1 | 67 |
| Water Loss on E | UNIMOD:27 | 50 |
| Hydroxylation on N | UNIMOD:35 | 45 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 31 |
| Sodium on D | UNIMOD:30 | 31 |
| Sodium on E | UNIMOD:30 | 31 |
| Methylation on K | UNIMOD:34 | 29 |
| Carbamyl on M | UNIMOD:5 | 25 |
| N-acetylserine on S | UNIMOD:1 | 23 |
| Hydroxylation on K | UNIMOD:35 | 22 |
| N-acetylmethionine on M | UNIMOD:1 | 22 |
| Acetylation on K | UNIMOD:1 | 20 |
| Acetylation on X | UNIMOD:1 | 19 |
| Magnesium on E | UNIMOD:956 | 19 |
| Fe[II] on D | UNIMOD:952 | 18 |
| HexNAc on T | UNIMOD:43 | 18 |
| 4-hydroxyproline on P | UNIMOD:35 | 14 |
| Fe[III] on E | UNIMOD:1870 | 13 |
| N6-acetyllysine on K | UNIMOD:1 | 13 |
| Phosphoserine on S | UNIMOD:21 | 12 |
| Carbamyl on K | UNIMOD:5 | 11 |
| HexNAc on S | UNIMOD:43 | 11 |
| N5-methylglutamine on Q | UNIMOD:34 | 10 |
| Omega-N-methylarginine on R | UNIMOD:34 | 10 |
| Methylation on R | UNIMOD:34 | 9 |
| Dimethylation on K | UNIMOD:36 | 8 |
| Magnesium on D | UNIMOD:956 | 8 |
| N-acetylthreonine on T | UNIMOD:1 | 8 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 8 |
| Deamidated asparagine on N | UNIMOD:7 | 7 |
| Fe[III] on D | UNIMOD:1870 | 6 |
| Fe[II] on E | UNIMOD:952 | 6 |
| Glutarylation on K | UNIMOD:1848 | 6 |
| HexNAc on Nxs | UNIMOD:43 | 6 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 6 |
| N6-methyllysine on K | UNIMOD:34 | 6 |
| Phosphorylation on S | UNIMOD:21 | 6 |
| Carboxylation on E | UNIMOD:299 | 5 |
| Dimethylation on R | UNIMOD:36 | 5 |
| Formylation on K | UNIMOD:122 | 5 |
| HexNAc on Nxt | UNIMOD:43 | 5 |
| Trimethylation on K | UNIMOD:37 | 5 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 4 |
| Carbamyl on C | UNIMOD:5 | 4 |
| N6-succinyllysine on K | — | 4 |
| Carbamyl on R | UNIMOD:5 | 3 |
| Carboxylation on D | UNIMOD:299 | 3 |
| Citrulline on R | UNIMOD:7 | 3 |
| Phosphothreonine on T | UNIMOD:21 | 3 |
| Tele-methylhistidine on H | UNIMOD:34 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Butyrylation on K | UNIMOD:1289 | 2 |
| Carboxylation on K | UNIMOD:299 | 2 |
| Malonylation on K | UNIMOD:747 | 2 |
| N6-crotonyllysine on K | — | 2 |
| ADP-ribosylation on S | UNIMOD:213 | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxybutyrylation on K | — | 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 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| Nitrosylation on Y | UNIMOD:354 | 1 |
| Phosphorylation on T | UNIMOD:21 | 1 |
| Phosphorylation on Y | UNIMOD:21 | 1 |
| Phosphotyrosine on Y | UNIMOD:21 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 1 |
| Succinylation on K | UNIMOD:64 | 1 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 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
4114856412d41d9a, written 2026-10-29T11:07:55+00:00 by ingester 1.4.0- Reconciliation
- every check agreed with the producer's own counts
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group