Generated summary
PXD006898 is a DDA label-free dataset (Homo sapiens) with 15 runs, 15 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 618,984 PSMs, 61,755 peptidoforms and 6,520 protein groups, and the repository holds 31,076 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
count_mismatch warning
The bundle holds 61755 where the producer reported 61754 (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 61755 where the producer reported 61754 (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 618984 where the producer reported 619019 (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 618984 where the producer reported 619019 (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.
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 71817 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 8137 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 71817 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 8137 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: 2020 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: 2020 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: 4 identifier(s), 7 row(s) dropped, e.g. PXD006898:A0A1B0GTS1;A0A1B0GWH4 written 2 times; quant_values: 60 identifier(s), 105 row(s) dropped, e.g. PXD006898:070215D108_1:label_free:protein_group:PXD006898:A0A1B0GTS1;A0A1B0GWH4: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: 4 identifier(s), 7 row(s) dropped, e.g. PXD006898:A0A1B0GTS1;A0A1B0GWH4 written 2 times; quant_values: 60 identifier(s), 105 row(s) dropped, e.g. PXD006898:070215D108_1:label_free:protein_group:PXD006898:A0A1B0GTS1;A0A1B0GWH4:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
86 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
86 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 | 618,984 |
| Peptidoforms at 1% FDR | 61,755 |
| Protein groups at 1% FDR | 6,520 |
| PTM sites | 31,076 |
| Quantitative values | 597,510 |
| PSMs, all (including decoys and sub-threshold) | 826,160 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 69.7% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.4% |
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
- 15 / 15
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 12,104 |
| Oxidation on M | UNIMOD:35 | 4,558 |
| Deamidation on N | UNIMOD:7 | 4,181 |
| Deamidation on Q | UNIMOD:7 | 3,532 |
| Hydroxylation on P | UNIMOD:35 | 755 |
| Citrullination on R | UNIMOD:7 | 638 |
| Ammonia loss on N | UNIMOD:385 | 494 |
| Phosphoserine on S | UNIMOD:21 | 399 |
| N-acetylalanine on A | UNIMOD:1 | 306 |
| Hydroxylation on N | UNIMOD:35 | 272 |
| Ammonia loss on C | UNIMOD:385 | 269 |
| Methylation on K | UNIMOD:34 | 210 |
| Carbamyl on X | UNIMOD:5 | 201 |
| Hydroxylation on K | UNIMOD:35 | 159 |
| N-acetylmethionine on M | UNIMOD:1 | 159 |
| Sodium on E | UNIMOD:30 | 139 |
| Acetylation on X | UNIMOD:1 | 137 |
| Sodium on D | UNIMOD:30 | 131 |
| N-acetylserine on S | UNIMOD:1 | 117 |
| Phosphorylation on S | UNIMOD:21 | 102 |
| Methylation on R | UNIMOD:34 | 94 |
| Magnesium on D | UNIMOD:956 | 86 |
| Dimethylation on K | UNIMOD:36 | 75 |
| Magnesium on E | UNIMOD:956 | 69 |
| Phosphothreonine on T | UNIMOD:21 | 68 |
| Dimethylation on R | UNIMOD:36 | 63 |
| Phosphorylation on T | UNIMOD:21 | 61 |
| Water Loss on E | UNIMOD:27 | 61 |
| Calcium on E | UNIMOD:951 | 60 |
| N6-acetyllysine on K | UNIMOD:1 | 59 |
| 4-hydroxyproline on P | UNIMOD:35 | 57 |
| Acetylation on K | UNIMOD:1 | 54 |
| Omega-N-methylarginine on R | UNIMOD:34 | 54 |
| Calcium on D | UNIMOD:951 | 49 |
| HexNAc on S | UNIMOD:43 | 47 |
| Trimethylation on K | UNIMOD:37 | 37 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 36 |
| Carbamyl on K | UNIMOD:5 | 36 |
| Carbamyl on M | UNIMOD:5 | 35 |
| HexNAc on T | UNIMOD:43 | 33 |
| Carboxylation on E | UNIMOD:299 | 30 |
| N6-methyllysine on K | UNIMOD:34 | 27 |
| N-acetylthreonine on T | UNIMOD:1 | 26 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 26 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 24 |
| Formylation on K | UNIMOD:122 | 22 |
| Glutarylation on K | UNIMOD:1848 | 20 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 20 |
| Deamidated asparagine on N | UNIMOD:7 | 19 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 19 |
| Succinylation on K | UNIMOD:64 | 17 |
| N6-succinyllysine on K | — | 16 |
| Sulfonation on Y | UNIMOD:40 | 16 |
| Carbamyl on R | UNIMOD:5 | 15 |
| Carboxylation on D | UNIMOD:299 | 15 |
| Hydroxybutyrylation on K | — | 15 |
| Phosphotyrosine on Y | UNIMOD:21 | 15 |
| Butyrylation on K | UNIMOD:1289 | 14 |
| Nitrosylation on Y | UNIMOD:354 | 14 |
| Potassium on E | UNIMOD:530 | 14 |
| Phosphorylation on Y | UNIMOD:21 | 13 |
| Carboxylation on K | UNIMOD:299 | 12 |
| Nitrosylation on C | UNIMOD:275 | 12 |
| Potassium on D | UNIMOD:530 | 12 |
| Malonylation on K | UNIMOD:747 | 11 |
| Carbamyl on C | UNIMOD:5 | 10 |
| Cu[I] on E | UNIMOD:531 | 10 |
| Fe[III] on D | UNIMOD:1870 | 10 |
| Fe[II] on E | UNIMOD:952 | 10 |
| Crotonylation on K | UNIMOD:1363 | 8 |
| Fe[II] on D | UNIMOD:952 | 7 |
| Citrulline on R | UNIMOD:7 | 6 |
| Dimethylated arginine on R | UNIMOD:36 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| N6-butyryllysine on K | UNIMOD:1289 | 6 |
| S-nitrosocysteine on C | UNIMOD:275 | 6 |
| Cu[I] on D | UNIMOD:531 | 5 |
| Fe[III] on E | UNIMOD:1870 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| N6-glutaryllysine on K | — | 3 |
| Zinc on E | UNIMOD:954 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N6-methacryllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| S-farnesyl cysteine on C | UNIMOD:44 | 2 |
| Zinc on D | UNIMOD:954 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 2,3-didehydroalanine (Ser) on S | UNIMOD:23 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 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
a9a0af41098d8d13, written 2026-10-29T10:46:37+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