Generated summary
PXD009430 is a DDA label-free dataset (Homo sapiens) with 12 runs, 12 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 301,057 PSMs, 20,480 peptidoforms and 2,782 protein groups, and the repository holds 16,167 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 301057 where the producer reported 301104 (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 301057 where the producer reported 301104 (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 58940 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4072 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 58940 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4072 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 71 to 72 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD009430\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-01-41-09.msp and has NOT been registered, so nothing was lost; merge it deliberately.
human's current library moved from version 71 to 72 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD009430\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-24-01-41-09.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: 944 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: 944 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), 15 row(s) dropped, e.g. PXD009430:A0A087WUL8;A0AAG2SUX2;A0AAG2UXD8;A0AAG2UXK7;A0AAG2UXS2;P0DPF3;Q3BBV0;Q3BBV2;Q5TAG4;Q5TI25;Q6P3W6;Q86T75;Q8N660 written 7 times; quant_values: 48 identifier(s), 180 row(s) dropped, e.g. PXD009430:mm131128_01:label_free:protein_group:PXD009430:A0A087WUL8;A0AAG2SUX2;A0AAG2UXD8;A0AAG2UXK7;A0AAG2UXS2;P0DPF3;Q3BBV0;Q3BBV2;Q5TAG4;Q5TI25;Q6P3W6;Q86T75;Q8N660:QuantProject:DEF-PROT-SPC written 7 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), 15 row(s) dropped, e.g. PXD009430:A0A087WUL8;A0AAG2SUX2;A0AAG2UXD8;A0AAG2UXK7;A0AAG2UXS2;P0DPF3;Q3BBV0;Q3BBV2;Q5TAG4;Q5TI25;Q6P3W6;Q86T75;Q8N660 written 7 times; quant_values: 48 identifier(s), 180 row(s) dropped, e.g. PXD009430:mm131128_01:label_free:protein_group:PXD009430:A0A087WUL8;A0AAG2SUX2;A0AAG2UXD8;A0AAG2UXK7;A0AAG2UXS2;P0DPF3;Q3BBV0;Q3BBV2;Q5TAG4;Q5TI25;Q6P3W6;Q86T75;Q8N660:QuantProject:DEF-PROT-SPC written 7 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
60 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
60 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 | 301,057 |
| Peptidoforms at 1% FDR | 20,480 |
| Protein groups at 1% FDR | 2,782 |
| PTM sites | 16,167 |
| Quantitative values | 255,719 |
| PSMs, all (including decoys and sub-threshold) | 686,587 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 74.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.8% |
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
- 12 / 12
- 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 |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 4,234 |
| Carbamidomethyl on C | UNIMOD:4 | 3,940 |
| Deamidation on N | UNIMOD:7 | 2,458 |
| Deamidation on Q | UNIMOD:7 | 1,724 |
| Hydroxylation on P | UNIMOD:35 | 382 |
| Citrullination on R | UNIMOD:7 | 308 |
| N-acetylalanine on A | UNIMOD:1 | 190 |
| Ammonia loss on N | UNIMOD:385 | 176 |
| Hydroxylation on N | UNIMOD:35 | 152 |
| Phosphoserine on S | UNIMOD:21 | 129 |
| Magnesium on E | UNIMOD:956 | 96 |
| Carbamyl on X | UNIMOD:5 | 93 |
| Sodium on E | UNIMOD:30 | 91 |
| Ammonia loss on C | UNIMOD:385 | 90 |
| Magnesium on D | UNIMOD:956 | 87 |
| Sodium on D | UNIMOD:30 | 71 |
| Methylation on K | UNIMOD:34 | 69 |
| Hydroxylation on K | UNIMOD:35 | 68 |
| N-acetylmethionine on M | UNIMOD:1 | 63 |
| N-acetylserine on S | UNIMOD:1 | 63 |
| Water Loss on E | UNIMOD:27 | 58 |
| Dimethylation on K | UNIMOD:36 | 52 |
| N6-acetyllysine on K | UNIMOD:1 | 51 |
| Dimethylation on R | UNIMOD:36 | 48 |
| Phosphorylation on S | UNIMOD:21 | 38 |
| Formylation on K | UNIMOD:122 | 35 |
| Methylation on R | UNIMOD:34 | 35 |
| HexNAc on S | UNIMOD:43 | 28 |
| Acetylation on X | UNIMOD:1 | 26 |
| Phosphorylation on T | UNIMOD:21 | 26 |
| Acetylation on K | UNIMOD:1 | 25 |
| Phosphothreonine on T | UNIMOD:21 | 25 |
| Carboxylation on D | UNIMOD:299 | 24 |
| Carbamyl on M | UNIMOD:5 | 21 |
| Omega-N-methylarginine on R | UNIMOD:34 | 21 |
| HexNAc on T | UNIMOD:43 | 20 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 19 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 18 |
| Calcium on D | UNIMOD:951 | 18 |
| Trimethylation on K | UNIMOD:37 | 16 |
| Calcium on E | UNIMOD:951 | 14 |
| N-acetylthreonine on T | UNIMOD:1 | 13 |
| Carboxylation on E | UNIMOD:299 | 12 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 11 |
| Sulfonation on Y | UNIMOD:40 | 11 |
| Carbamyl on K | UNIMOD:5 | 10 |
| N6-methyllysine on K | UNIMOD:34 | 10 |
| N6-succinyllysine on K | — | 9 |
| Potassium on D | UNIMOD:530 | 9 |
| 4-hydroxyproline on P | UNIMOD:35 | 8 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 8 |
| Malonylation on K | UNIMOD:747 | 8 |
| Nitrosylation on Y | UNIMOD:354 | 8 |
| Phosphorylation on Y | UNIMOD:21 | 8 |
| Potassium on E | UNIMOD:530 | 7 |
| Dimethylated arginine on R | UNIMOD:36 | 6 |
| Phosphotyrosine on Y | UNIMOD:21 | 6 |
| Succinylation on K | UNIMOD:64 | 6 |
| Carbamyl on C | UNIMOD:5 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Crotonylation on K | UNIMOD:1363 | 4 |
| Hydroxybutyrylation on K | — | 4 |
| Butyrylation on K | UNIMOD:1289 | 3 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Glutarylation on K | UNIMOD:1848 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N-acetylglycine on G | UNIMOD:1 | 3 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 3 |
| N6-glutaryllysine on K | — | 3 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| Nitrosylation on C | UNIMOD:275 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carbamyl on R | UNIMOD:5 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 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
8b3c8ba5668854e9, written 2026-10-29T11:02:40+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