Generated summary
PXD030939 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and runs that differ in enrichment (phospho on some runs; see each run's own). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,169,720 PSMs, 125,414 peptidoforms and 7,958 protein groups, and the repository holds 75,247 PTM sites for it. 6 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, 6 warnings and 2 for information
count_mismatch warning
The bundle holds 1.16972e+06 where the producer reported 1.17001e+06 (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 1.16972e+06 where the producer reported 1.17001e+06 (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.
low_core_use warning
13.73 avg cores of 32 allowed (S5)
13.73 avg cores of 32 allowed (S5)
mixed_enrichment warning
The runs of this dataset differ in enrichment: 10 run(s) [none]; 10 run(s) [phospho]. The dataset's own `enrichment` is the producer's declaration and is true of only some runs, so answer any enrichment-dependent question per run from `runs.enrichment`, and never pool its runs as one kind.
The runs of this dataset differ in enrichment: 10 run(s) [none]; 10 run(s) [phospho]. The dataset's own `enrichment` is the producer's declaration and is true of only some runs, so answer any enrichment-dependent question per run from `runs.enrichment`, and never pool its runs as one kind.
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 334736 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 59 duplicate entry for one site and run (identical values; same protein group); 10298 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 334736 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 59 duplicate entry for one site and run (identical values; same protein group); 10298 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: 2629 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: 2629 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: 7 identifier(s), 15 row(s) dropped, e.g. PXD030939:A0AAG2UXZ5;P39060 written 2 times; quant_values: 140 identifier(s), 300 row(s) dropped, e.g. PXD030939:Q1_ColID_292_2641_pp01:label_free:protein_group:PXD030939:A0AAG2UXZ5;P39060: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: 7 identifier(s), 15 row(s) dropped, e.g. PXD030939:A0AAG2UXZ5;P39060 written 2 times; quant_values: 140 identifier(s), 300 row(s) dropped, e.g. PXD030939:Q1_ColID_292_2641_pp01:label_free:protein_group:PXD030939:A0AAG2UXZ5;P39060:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
187 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
187 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 | 1,169,720 |
| Peptidoforms at 1% FDR | 125,414 |
| Protein groups at 1% FDR | 7,958 |
| PTM sites | 75,247 |
| Quantitative values | 1,137,417 |
| PSMs, all (including decoys and sub-threshold) | 1,526,779 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 76.6% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.3% |
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
- phospho (on some runs only; runs differ)
- Instrument vendor
- not recorded
- Runs / samples
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- b8b36ebf6016
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 21,701 |
| Phosphoserine on S | UNIMOD:21 | 9,390 |
| Phosphorylation on S | UNIMOD:21 | 8,875 |
| Oxidation on M | UNIMOD:35 | 8,325 |
| Deamidation on N | UNIMOD:7 | 5,365 |
| Deamidation on Q | UNIMOD:7 | 3,602 |
| Phosphorylation on T | UNIMOD:21 | 3,155 |
| Citrullination on R | UNIMOD:7 | 1,364 |
| Phosphothreonine on T | UNIMOD:21 | 1,189 |
| Phosphorylation on Y | UNIMOD:21 | 832 |
| Hydroxylation on P | UNIMOD:35 | 796 |
| Sulfonation on Y | UNIMOD:40 | 725 |
| Sodium on E | UNIMOD:30 | 622 |
| Ammonia loss on N | UNIMOD:385 | 608 |
| Magnesium on E | UNIMOD:956 | 578 |
| Sodium on D | UNIMOD:30 | 529 |
| Ammonia loss on C | UNIMOD:385 | 486 |
| Calcium on E | UNIMOD:951 | 453 |
| Magnesium on D | UNIMOD:956 | 440 |
| Calcium on D | UNIMOD:951 | 393 |
| N-acetylalanine on A | UNIMOD:1 | 388 |
| Hydroxylation on N | UNIMOD:35 | 380 |
| Carbamyl on X | UNIMOD:5 | 297 |
| N-acetylmethionine on M | UNIMOD:1 | 228 |
| Potassium on E | UNIMOD:530 | 203 |
| Potassium on D | UNIMOD:530 | 178 |
| Methylation on K | UNIMOD:34 | 171 |
| Acetylation on X | UNIMOD:1 | 167 |
| Hydroxylation on K | UNIMOD:35 | 163 |
| Water Loss on E | UNIMOD:27 | 158 |
| Methylation on R | UNIMOD:34 | 154 |
| N-acetylserine on S | UNIMOD:1 | 138 |
| Phosphotyrosine on Y | UNIMOD:21 | 133 |
| Succinylation on K | UNIMOD:64 | 112 |
| Omega-N-methylarginine on R | UNIMOD:34 | 105 |
| Dimethylation on R | UNIMOD:36 | 101 |
| Formylation on K | UNIMOD:122 | 96 |
| N6-acetyllysine on K | UNIMOD:1 | 86 |
| Fe[II] on E | UNIMOD:952 | 82 |
| Fe[III] on E | UNIMOD:1870 | 78 |
| Acetylation on K | UNIMOD:1 | 74 |
| Fe[III] on D | UNIMOD:1870 | 70 |
| Fe[II] on D | UNIMOD:952 | 69 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 62 |
| Dimethylation on K | UNIMOD:36 | 60 |
| Cu[I] on E | UNIMOD:531 | 59 |
| HexNAc on S | UNIMOD:43 | 59 |
| Malonylation on K | UNIMOD:747 | 55 |
| HexNAc on T | UNIMOD:43 | 53 |
| Crotonylation on K | UNIMOD:1363 | 50 |
| Carboxylation on E | UNIMOD:299 | 48 |
| Hydroxybutyrylation on K | — | 47 |
| Cu[I] on D | UNIMOD:531 | 43 |
| Carbamyl on K | UNIMOD:5 | 40 |
| Carboxylation on D | UNIMOD:299 | 40 |
| Carbamyl on M | UNIMOD:5 | 36 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 36 |
| N6-methyllysine on K | UNIMOD:34 | 36 |
| Trimethylation on K | UNIMOD:37 | 35 |
| Glutarylation on K | UNIMOD:1848 | 34 |
| Butyrylation on K | UNIMOD:1289 | 32 |
| N-acetylthreonine on T | UNIMOD:1 | 30 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 30 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 27 |
| Carbamyl on R | UNIMOD:5 | 26 |
| Nitrosylation on Y | UNIMOD:354 | 21 |
| ADP-ribosylation on S | UNIMOD:213 | 19 |
| Pyridoxal phosphate on K | UNIMOD:46 | 18 |
| Zinc on E | UNIMOD:954 | 18 |
| Carboxylation on K | UNIMOD:299 | 17 |
| 4-hydroxyproline on P | UNIMOD:35 | 15 |
| N6-succinyllysine on K | — | 15 |
| Nitrosylation on C | UNIMOD:275 | 14 |
| Zinc on D | UNIMOD:954 | 14 |
| N6-glutaryllysine on K | — | 11 |
| Carbamyl on C | UNIMOD:5 | 10 |
| Dimethylated arginine on R | UNIMOD:36 | 10 |
| Citrulline on R | UNIMOD:7 | 8 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| Deamidated asparagine on N | UNIMOD:7 | 7 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| Methionine (R)-sulfoxide on M | UNIMOD:35 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-crotonyllysine on K | — | 5 |
| S-nitrosocysteine on C | UNIMOD:275 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N-myristoyl glycine on G | UNIMOD:45 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| N,N,N-trimethylglycine on G | — | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| (3S)-3-hydroxylysine on K | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| S-farnesyl cysteine on C | UNIMOD:44 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-carboxyglutamate on E | UNIMOD:299 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-carboxylysine on K | UNIMOD:299 | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 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
dae786777fe1d0dc, written 2026-10-29T12:42:02+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