Generated summary
PXD028975 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 563,284 PSMs, 15,864 peptidoforms and 2,055 protein groups, and the repository holds 18,331 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 563284 where the producer reported 563549 (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 563284 where the producer reported 563549 (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
32.26% of protein intensity in the worst file, 22.90% median across 30 files (DEF-QC-9 v3.5)
32.26% of protein intensity in the worst file, 22.90% 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 69081 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 duplicate entry for one site and run (identical values; same protein group); 407 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 69081 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2 duplicate entry for one site and run (identical values; same protein group); 407 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).
spectral_library warning
human's current library moved from version 72 to 73 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD028975\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-05-53-41.msp and has NOT been registered, so nothing was lost; merge it deliberately.
human's current library moved from version 72 to 73 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD028975\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-05-53-41.msp and has NOT been registered, so nothing was lost; merge it deliberately.
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: 1129 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: 1129 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), 3 row(s) dropped, e.g. PXD028975:A0A590UK10;Q6ZSZ5 written 2 times; quant_values: 60 identifier(s), 90 row(s) dropped, e.g. PXD028975:20210730_DM_2D_1_1:label_free:protein_group:PXD028975:A0A590UK10;Q6ZSZ5: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), 3 row(s) dropped, e.g. PXD028975:A0A590UK10;Q6ZSZ5 written 2 times; quant_values: 60 identifier(s), 90 row(s) dropped, e.g. PXD028975:20210730_DM_2D_1_1:label_free:protein_group:PXD028975:A0A590UK10;Q6ZSZ5:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
214 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
214 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 | 563,284 |
| Peptidoforms at 1% FDR | 15,864 |
| Protein groups at 1% FDR | 2,055 |
| PTM sites | 18,331 |
| Quantitative values | 303,683 |
| PSMs, all (including decoys and sub-threshold) | 2,217,926 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 26.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 22.1% |
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-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 6,092 |
| Oxidation on M | UNIMOD:35 | 1,696 |
| Deamidation on N | UNIMOD:7 | 1,693 |
| Deamidation on Q | UNIMOD:7 | 1,153 |
| Hydroxylation on P | UNIMOD:35 | 947 |
| Citrullination on R | UNIMOD:7 | 422 |
| Ammonia loss on N | UNIMOD:385 | 380 |
| Hydroxylation on N | UNIMOD:35 | 304 |
| Fe[III] on E | UNIMOD:1870 | 201 |
| Fe[III] on D | UNIMOD:1870 | 191 |
| Hydroxylation on K | UNIMOD:35 | 171 |
| Ammonia loss on C | UNIMOD:385 | 165 |
| Methylation on R | UNIMOD:34 | 165 |
| Phosphoserine on S | UNIMOD:21 | 164 |
| 4-hydroxyproline on P | UNIMOD:35 | 160 |
| Sodium on E | UNIMOD:30 | 155 |
| Calcium on E | UNIMOD:951 | 153 |
| Methylation on K | UNIMOD:34 | 151 |
| Magnesium on E | UNIMOD:956 | 132 |
| Calcium on D | UNIMOD:951 | 126 |
| Phosphorylation on S | UNIMOD:21 | 126 |
| Fe[II] on E | UNIMOD:952 | 116 |
| Magnesium on D | UNIMOD:956 | 116 |
| Sodium on D | UNIMOD:30 | 112 |
| Formylation on K | UNIMOD:122 | 105 |
| Fe[II] on D | UNIMOD:952 | 104 |
| Potassium on E | UNIMOD:530 | 97 |
| Phosphorylation on T | UNIMOD:21 | 71 |
| Potassium on D | UNIMOD:530 | 69 |
| Acetylation on K | UNIMOD:1 | 67 |
| Water Loss on E | UNIMOD:27 | 63 |
| Dimethylation on K | UNIMOD:36 | 58 |
| Carboxylation on E | UNIMOD:299 | 52 |
| Dimethylation on R | UNIMOD:36 | 52 |
| N6-acetyllysine on K | UNIMOD:1 | 45 |
| Cu[I] on E | UNIMOD:531 | 38 |
| Carbamyl on X | UNIMOD:5 | 35 |
| Phosphothreonine on T | UNIMOD:21 | 33 |
| HexNAc on T | UNIMOD:43 | 32 |
| N-acetylalanine on A | UNIMOD:1 | 32 |
| HexNAc on S | UNIMOD:43 | 28 |
| Carboxylation on D | UNIMOD:299 | 27 |
| Cu[I] on D | UNIMOD:531 | 26 |
| Nitrosylation on C | UNIMOD:275 | 26 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 23 |
| N-acetylserine on S | UNIMOD:1 | 19 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 19 |
| Zinc on D | UNIMOD:954 | 19 |
| Sulfonation on Y | UNIMOD:40 | 18 |
| Zinc on E | UNIMOD:954 | 17 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 16 |
| Nitrosylation on Y | UNIMOD:354 | 16 |
| Trimethylation on K | UNIMOD:37 | 15 |
| Carbamyl on M | UNIMOD:5 | 14 |
| N6-methyllysine on K | UNIMOD:34 | 14 |
| Phosphorylation on Y | UNIMOD:21 | 14 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 13 |
| Carbamyl on C | UNIMOD:5 | 13 |
| N-acetylmethionine on M | UNIMOD:1 | 13 |
| Malonylation on K | UNIMOD:747 | 12 |
| Omega-N-methylarginine on R | UNIMOD:34 | 12 |
| Deamidated asparagine on N | UNIMOD:7 | 11 |
| Glutarylation on K | UNIMOD:1848 | 10 |
| Carbamyl on K | UNIMOD:5 | 9 |
| Citrulline on R | UNIMOD:7 | 9 |
| 5-hydroxylysine on K | UNIMOD:35 | 7 |
| N6-succinyllysine on K | — | 7 |
| Acetylation on X | UNIMOD:1 | 6 |
| Crotonylation on K | UNIMOD:1363 | 6 |
| Hydroxyproline on P | UNIMOD:35 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Butyrylation on K | UNIMOD:1289 | 5 |
| Carboxylation on K | UNIMOD:299 | 5 |
| Hydroxybutyrylation on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| (3R)-3-hydroxyasparagine on N | UNIMOD:35 | 3 |
| 3-hydroxyproline on P | UNIMOD:35 | 3 |
| HexNAc on Nxt | UNIMOD:43 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-acetylthreonine on T | UNIMOD:1 | 2 |
| N-acetylvaline on V | UNIMOD:1 | 2 |
| N-myristoyl glycine on G | UNIMOD:45 | 2 |
| 3'-nitrotyrosine on Y | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylglycine on G | UNIMOD:1 | 1 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
c5ad2715fc9a391f, written 2026-10-29T12:21:11+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