Generated summary
PXD019279 is a DDA label-free dataset (Homo sapiens) with 51 runs, 51 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,665,837 PSMs, 56,523 peptidoforms and 5,256 protein groups, and the repository holds 46,224 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 56523 where the producer reported 56522 (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 56523 where the producer reported 56522 (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 1.66584e+06 where the producer reported 1.66604e+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 1.66584e+06 where the producer reported 1.66604e+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.
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 322373 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 29350 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 322373 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 29350 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: 10137 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: 10137 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: 5 identifier(s), 6 row(s) dropped, e.g. PXD019279:A1L443;A6NNL0;Q5VT03;Q5VZR2;Q8IVF1 written 3 times; quant_values: 255 identifier(s), 306 row(s) dropped, e.g. PXD019279:Lewy2_10Cs_2Nov13_Samwise_13-07-28:label_free:protein_group:PXD019279:A1L443;A6NNL0;Q5VT03;Q5VZR2;Q8IVF1: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: 5 identifier(s), 6 row(s) dropped, e.g. PXD019279:A1L443;A6NNL0;Q5VT03;Q5VZR2;Q8IVF1 written 3 times; quant_values: 255 identifier(s), 306 row(s) dropped, e.g. PXD019279:Lewy2_10Cs_2Nov13_Samwise_13-07-28:label_free:protein_group:PXD019279:A1L443;A6NNL0;Q5VT03;Q5VZR2;Q8IVF1:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
134 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
134 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 | 1,665,837 |
| Peptidoforms at 1% FDR | 56,523 |
| Protein groups at 1% FDR | 5,256 |
| PTM sites | 46,224 |
| Quantitative values | 2,351,834 |
| PSMs, all (including decoys and sub-threshold) | 3,285,388 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 86.0% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.2% |
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
- 51 / 51
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0ba5e4c3fd33
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 13,037 |
| Oxidation on M | UNIMOD:35 | 4,446 |
| Deamidation on Q | UNIMOD:7 | 4,412 |
| Deamidation on N | UNIMOD:7 | 3,943 |
| Carbamyl on X | UNIMOD:5 | 2,233 |
| Fe[III] on E | UNIMOD:1870 | 1,684 |
| Citrullination on R | UNIMOD:7 | 1,656 |
| Hydroxylation on P | UNIMOD:35 | 1,454 |
| Fe[III] on D | UNIMOD:1870 | 1,419 |
| Ammonia loss on N | UNIMOD:385 | 796 |
| Hydroxylation on N | UNIMOD:35 | 725 |
| Fe[II] on E | UNIMOD:952 | 560 |
| Fe[II] on D | UNIMOD:952 | 507 |
| Sodium on E | UNIMOD:30 | 466 |
| Magnesium on E | UNIMOD:956 | 446 |
| Magnesium on D | UNIMOD:956 | 433 |
| Hydroxylation on K | UNIMOD:35 | 432 |
| Sodium on D | UNIMOD:30 | 412 |
| Phosphoserine on S | UNIMOD:21 | 387 |
| Carbamyl on M | UNIMOD:5 | 383 |
| Acetylation on K | UNIMOD:1 | 374 |
| Methylation on K | UNIMOD:34 | 365 |
| Carbamyl on K | UNIMOD:5 | 322 |
| Ammonia loss on C | UNIMOD:385 | 315 |
| N-acetylalanine on A | UNIMOD:1 | 280 |
| Methylation on R | UNIMOD:34 | 223 |
| Carbamyl on R | UNIMOD:5 | 201 |
| N6-acetyllysine on K | UNIMOD:1 | 191 |
| Calcium on E | UNIMOD:951 | 184 |
| Calcium on D | UNIMOD:951 | 176 |
| Acetylation on X | UNIMOD:1 | 170 |
| Phosphorylation on S | UNIMOD:21 | 167 |
| Trimethylation on K | UNIMOD:37 | 158 |
| Dimethylation on K | UNIMOD:36 | 145 |
| Phosphorylation on T | UNIMOD:21 | 142 |
| Carboxylation on E | UNIMOD:299 | 129 |
| Dimethylation on R | UNIMOD:36 | 129 |
| 4-hydroxyproline on P | UNIMOD:35 | 125 |
| N-acetylmethionine on M | UNIMOD:1 | 124 |
| Carboxylation on D | UNIMOD:299 | 119 |
| Water Loss on E | UNIMOD:27 | 117 |
| Carbamyl on C | UNIMOD:5 | 114 |
| N-acetylserine on S | UNIMOD:1 | 114 |
| Phosphothreonine on T | UNIMOD:21 | 113 |
| Potassium on D | UNIMOD:530 | 91 |
| Potassium on E | UNIMOD:530 | 78 |
| Crotonylation on K | UNIMOD:1363 | 72 |
| Nitrosylation on Y | UNIMOD:354 | 71 |
| HexNAc on T | UNIMOD:43 | 60 |
| Succinylation on K | UNIMOD:64 | 59 |
| Butyrylation on K | UNIMOD:1289 | 58 |
| N6-succinyllysine on K | — | 58 |
| Omega-N-methylarginine on R | UNIMOD:34 | 58 |
| Glutarylation on K | UNIMOD:1848 | 56 |
| HexNAc on S | UNIMOD:43 | 55 |
| Carboxylation on K | UNIMOD:299 | 54 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 45 |
| Malonylation on K | UNIMOD:747 | 44 |
| Formylation on K | UNIMOD:122 | 43 |
| Sulfonation on Y | UNIMOD:40 | 36 |
| Hydroxybutyrylation on K | — | 35 |
| Phosphorylation on Y | UNIMOD:21 | 35 |
| N-myristoyl glycine on G | UNIMOD:45 | 29 |
| Cu[I] on D | UNIMOD:531 | 28 |
| Cu[I] on E | UNIMOD:531 | 28 |
| N-acetylthreonine on T | UNIMOD:1 | 28 |
| Nitrosylation on C | UNIMOD:275 | 25 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 24 |
| Phosphotyrosine on Y | UNIMOD:21 | 17 |
| ADP-ribosylation on S | UNIMOD:213 | 15 |
| Citrulline on R | UNIMOD:7 | 15 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| N6-methyllysine on K | UNIMOD:34 | 15 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 14 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 14 |
| 5-hydroxylysine on K | UNIMOD:35 | 10 |
| Pyridoxal phosphate on K | UNIMOD:46 | 8 |
| Hydroxyproline on P | UNIMOD:35 | 7 |
| S-nitrosocysteine on C | UNIMOD:275 | 7 |
| Zinc on D | UNIMOD:954 | 7 |
| Zinc on E | UNIMOD:954 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 6 |
| N6-crotonyllysine on K | — | 5 |
| N6-methacryllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| N6-glutaryllysine on K | — | 4 |
| 3'-nitrotyrosine on Y | — | 3 |
| Allysine on K | UNIMOD:352 | 3 |
| Deamidated glutamine on Q | UNIMOD:7 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 2 |
| N6-malonyllysine on K | — | 2 |
| S-farnesyl cysteine on C | UNIMOD:44 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfenic acid (-SOH) on C | UNIMOD:35 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N5-methylglutamine on Q | UNIMOD:34 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| O-(pantetheine 4'-phosphoryl)serine on S | UNIMOD:49 | 1 |
| O-AMP-tyrosine on Y | UNIMOD:405 | 1 |
| O-palmitoyl serine on S | UNIMOD:47 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 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
638e9bdfb7324294, written 2026-10-29T11:20:19+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