Generated summary
PXD030773 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 847,058 PSMs, 72,404 peptidoforms and 5,942 protein groups, and the repository holds 35,306 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 847058 where the producer reported 847082 (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 847058 where the producer reported 847082 (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
7.20% of protein intensity in the worst file, 3.15% median across 30 files (DEF-QC-9 v3.5)
7.20% of protein intensity in the worst file, 3.15% median across 30 files (DEF-QC-9 v3.5)
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 129840 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9645 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 129840 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9645 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: 7314 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: 7314 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), 2 row(s) dropped, e.g. PXD030773:A8MPP1;Q92771;Q96FC9 written 3 times; quant_values: 31 identifier(s), 62 row(s) dropped, e.g. PXD030773:20151013_AWH_ColID_0_Ascyk_Herling_Ctrl_1_01:label_free:protein_group:PXD030773:A8MPP1;Q92771;Q96FC9:QuantProject:DEF-PROT-SPC written 3 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), 2 row(s) dropped, e.g. PXD030773:A8MPP1;Q92771;Q96FC9 written 3 times; quant_values: 31 identifier(s), 62 row(s) dropped, e.g. PXD030773:20151013_AWH_ColID_0_Ascyk_Herling_Ctrl_1_01:label_free:protein_group:PXD030773:A8MPP1;Q92771;Q96FC9:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
72 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
72 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 | 847,058 |
| Peptidoforms at 1% FDR | 72,404 |
| Protein groups at 1% FDR | 5,942 |
| PTM sites | 35,306 |
| Quantitative values | 866,235 |
| PSMs, all (including decoys and sub-threshold) | 1,617,322 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 53.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 3.7% |
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
- 30 / 30
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 9df4ce025f23
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,955 |
| Oxidation on M | UNIMOD:35 | 6,113 |
| Carbamyl on X | UNIMOD:5 | 2,780 |
| Deamidation on N | UNIMOD:7 | 2,027 |
| Deamidation on Q | UNIMOD:7 | 1,132 |
| Carbamyl on K | UNIMOD:5 | 548 |
| Citrullination on R | UNIMOD:7 | 530 |
| Ammonia loss on N | UNIMOD:385 | 476 |
| Hydroxylation on P | UNIMOD:35 | 474 |
| Phosphoserine on S | UNIMOD:21 | 409 |
| Hydroxylation on N | UNIMOD:35 | 401 |
| Fe[III] on E | UNIMOD:1870 | 379 |
| Hydroxylation on K | UNIMOD:35 | 323 |
| Ammonia loss on C | UNIMOD:385 | 315 |
| N-acetylalanine on A | UNIMOD:1 | 298 |
| Fe[III] on D | UNIMOD:1870 | 284 |
| Water Loss on E | UNIMOD:27 | 283 |
| Sodium on E | UNIMOD:30 | 191 |
| Calcium on E | UNIMOD:951 | 189 |
| Methylation on K | UNIMOD:34 | 187 |
| Fe[II] on E | UNIMOD:952 | 157 |
| Acetylation on X | UNIMOD:1 | 153 |
| Methylation on R | UNIMOD:34 | 153 |
| Formylation on K | UNIMOD:122 | 150 |
| Phosphorylation on S | UNIMOD:21 | 150 |
| Acetylation on K | UNIMOD:1 | 149 |
| Carbamyl on R | UNIMOD:5 | 147 |
| Magnesium on E | UNIMOD:956 | 138 |
| N-acetylmethionine on M | UNIMOD:1 | 137 |
| Nitrosylation on Y | UNIMOD:354 | 127 |
| Calcium on D | UNIMOD:951 | 124 |
| Carbamyl on M | UNIMOD:5 | 124 |
| Sodium on D | UNIMOD:30 | 123 |
| N-acetylserine on S | UNIMOD:1 | 113 |
| Potassium on E | UNIMOD:530 | 110 |
| Magnesium on D | UNIMOD:956 | 95 |
| N6-acetyllysine on K | UNIMOD:1 | 94 |
| Fe[II] on D | UNIMOD:952 | 89 |
| Carboxylation on E | UNIMOD:299 | 76 |
| Dimethylation on K | UNIMOD:36 | 76 |
| Phosphorylation on T | UNIMOD:21 | 72 |
| Dimethylation on R | UNIMOD:36 | 59 |
| Potassium on D | UNIMOD:530 | 58 |
| Phosphothreonine on T | UNIMOD:21 | 53 |
| Carboxylation on D | UNIMOD:299 | 47 |
| HexNAc on T | UNIMOD:43 | 45 |
| Omega-N-methylarginine on R | UNIMOD:34 | 43 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 42 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 40 |
| Trimethylation on K | UNIMOD:37 | 40 |
| N6-methyllysine on K | UNIMOD:34 | 39 |
| Glutarylation on K | UNIMOD:1848 | 35 |
| Succinylation on K | UNIMOD:64 | 35 |
| HexNAc on S | UNIMOD:43 | 30 |
| Phosphorylation on Y | UNIMOD:21 | 29 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 27 |
| Hydroxybutyrylation on K | — | 25 |
| Carboxylation on K | UNIMOD:299 | 24 |
| Cu[I] on E | UNIMOD:531 | 21 |
| Malonylation on K | UNIMOD:747 | 21 |
| Crotonylation on K | UNIMOD:1363 | 20 |
| N-acetylthreonine on T | UNIMOD:1 | 20 |
| Sulfonation on Y | UNIMOD:40 | 19 |
| Carbamyl on C | UNIMOD:5 | 18 |
| Cu[I] on D | UNIMOD:531 | 16 |
| Butyrylation on K | UNIMOD:1289 | 15 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 15 |
| Deamidated asparagine on N | UNIMOD:7 | 14 |
| Phosphotyrosine on Y | UNIMOD:21 | 14 |
| Pyridoxal phosphate on K | UNIMOD:46 | 14 |
| 4-hydroxyproline on P | UNIMOD:35 | 12 |
| Zinc on D | UNIMOD:954 | 12 |
| N-acetylglycine on G | UNIMOD:1 | 11 |
| N6-succinyllysine on K | — | 11 |
| Nitrosylation on C | UNIMOD:275 | 8 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 7 |
| Dimethylated arginine on R | UNIMOD:36 | 6 |
| Zinc on E | UNIMOD:954 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-malonyllysine on K | — | 5 |
| N6-butyryllysine on K | UNIMOD:1289 | 4 |
| N6-glutaryllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Citrulline on R | UNIMOD:7 | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| (3S)-3-hydroxyasparagine on N | — | 2 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| ADP-ribosylation on S | UNIMOD:213 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| 5-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfenic acid (-SOH) on C | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
521b78bf8fcbbfc2, written 2026-10-29T12:24:44+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