Generated summary
PXD035299 is a DDA label-free dataset (Homo sapiens) with 10 runs, 10 samples and an enrichment step outside the controlled list (recorded as `other`). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,174,457 PSMs, 86,978 peptidoforms and 5,677 protein groups, and the repository holds 37,575 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 1.17446e+06 where the producer reported 1.17456e+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 1.17446e+06 where the producer reported 1.17456e+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 123289 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5219 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 123289 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5219 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 54 to 55 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD035299\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-13-08-22-40.msp and has NOT been registered, so nothing was lost; merge it deliberately.
human's current library moved from version 54 to 55 while this search was running. This run's library is at F:\aging_data\run_2026-09-21\PXD035299\04_search\mm\Task3SearchTask\updateSpectralLibrary_2026-10-13-08-22-40.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: 1278 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: 1278 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), 4 row(s) dropped, e.g. PXD035299:A0A5F9ZGT7;Q9H3S4 written 2 times; quant_values: 40 identifier(s), 40 row(s) dropped, e.g. PXD035299:b008p086_EVN_1_rpt:label_free:protein_group:PXD035299:A0A5F9ZGT7;Q9H3S4: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: 4 identifier(s), 4 row(s) dropped, e.g. PXD035299:A0A5F9ZGT7;Q9H3S4 written 2 times; quant_values: 40 identifier(s), 40 row(s) dropped, e.g. PXD035299:b008p086_EVN_1_rpt:label_free:protein_group:PXD035299:A0A5F9ZGT7;Q9H3S4:QuantProject:DEF-PROT-SPC written 2 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 | 1,174,457 |
| Peptidoforms at 1% FDR | 86,978 |
| Protein groups at 1% FDR | 5,677 |
| PTM sites | 37,575 |
| Quantitative values | 806,754 |
| PSMs, all (including decoys and sub-threshold) | 2,563,122 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 90.4% |
| 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
- other
- Instrument vendor
- not recorded
- Runs / samples
- 10 / 10
- 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 | 16,197 |
| Deamidation on N | UNIMOD:7 | 5,522 |
| Oxidation on M | UNIMOD:35 | 3,136 |
| Deamidation on Q | UNIMOD:7 | 2,737 |
| Phosphoserine on S | UNIMOD:21 | 1,899 |
| Ammonia loss on N | UNIMOD:385 | 853 |
| Phosphorylation on S | UNIMOD:21 | 718 |
| Citrullination on R | UNIMOD:7 | 602 |
| Hydroxylation on P | UNIMOD:35 | 532 |
| Carbamyl on K | UNIMOD:5 | 399 |
| Carbamyl on X | UNIMOD:5 | 379 |
| Ammonia loss on C | UNIMOD:385 | 333 |
| Phosphorylation on T | UNIMOD:21 | 311 |
| Water Loss on E | UNIMOD:27 | 311 |
| Formylation on K | UNIMOD:122 | 257 |
| Phosphothreonine on T | UNIMOD:21 | 230 |
| N-acetylalanine on A | UNIMOD:1 | 214 |
| Hydroxylation on N | UNIMOD:35 | 150 |
| Omega-N-methylarginine on R | UNIMOD:34 | 150 |
| Acetylation on X | UNIMOD:1 | 140 |
| N6-acetyllysine on K | UNIMOD:1 | 137 |
| HexNAc on S | UNIMOD:43 | 136 |
| 4-hydroxyproline on P | UNIMOD:35 | 135 |
| N-acetylmethionine on M | UNIMOD:1 | 130 |
| Hydroxylation on K | UNIMOD:35 | 120 |
| HexNAc on T | UNIMOD:43 | 117 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 96 |
| Methylation on K | UNIMOD:34 | 95 |
| Dimethylation on R | UNIMOD:36 | 93 |
| N-acetylserine on S | UNIMOD:1 | 92 |
| Sulfonation on Y | UNIMOD:40 | 85 |
| Phosphorylation on Y | UNIMOD:21 | 82 |
| Methylation on R | UNIMOD:34 | 68 |
| Acetylation on K | UNIMOD:1 | 51 |
| Magnesium on E | UNIMOD:956 | 50 |
| Sodium on E | UNIMOD:30 | 47 |
| Carbamyl on M | UNIMOD:5 | 40 |
| Dimethylation on K | UNIMOD:36 | 37 |
| Calcium on E | UNIMOD:951 | 36 |
| N6-methyllysine on K | UNIMOD:34 | 36 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 34 |
| Magnesium on D | UNIMOD:956 | 33 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 33 |
| Sodium on D | UNIMOD:30 | 33 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 25 |
| Phosphotyrosine on Y | UNIMOD:21 | 25 |
| Calcium on D | UNIMOD:951 | 22 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 20 |
| Potassium on E | UNIMOD:530 | 20 |
| N-acetylthreonine on T | UNIMOD:1 | 19 |
| Carbamyl on R | UNIMOD:5 | 14 |
| Deamidated asparagine on N | UNIMOD:7 | 14 |
| Fe[II] on E | UNIMOD:952 | 13 |
| N6-methacryllysine on K | — | 13 |
| N6-succinyllysine on K | — | 13 |
| Carboxylation on E | UNIMOD:299 | 12 |
| Carboxylation on K | UNIMOD:299 | 12 |
| Pyridoxal phosphate on K | UNIMOD:46 | 12 |
| Citrulline on R | UNIMOD:7 | 11 |
| Glutarylation on K | UNIMOD:1848 | 11 |
| Dimethylated arginine on R | UNIMOD:36 | 10 |
| Fe[III] on D | UNIMOD:1870 | 10 |
| Hydroxyproline on P | UNIMOD:35 | 9 |
| N6-glutaryllysine on K | — | 9 |
| Butyrylation on K | UNIMOD:1289 | 8 |
| Crotonylation on K | UNIMOD:1363 | 8 |
| Fe[III] on E | UNIMOD:1870 | 8 |
| Malonylation on K | UNIMOD:747 | 8 |
| Potassium on D | UNIMOD:530 | 8 |
| Hydroxybutyrylation on K | — | 7 |
| N6-crotonyllysine on K | — | 7 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 7 |
| 5-hydroxylysine on K | UNIMOD:35 | 6 |
| Fe[II] on D | UNIMOD:952 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| N5-methylglutamine on Q | UNIMOD:34 | 6 |
| Nitrosylation on C | UNIMOD:275 | 6 |
| Succinylation on K | UNIMOD:64 | 6 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 6 |
| Trimethylation on K | UNIMOD:37 | 6 |
| Nitrosylation on Y | UNIMOD:354 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 5 |
| Carboxylation on D | UNIMOD:299 | 4 |
| N6-butyryllysine on K | UNIMOD:1289 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Cysteine persulfide on C | UNIMOD:421 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 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
c34482064a766fdf, written 2026-10-29T12:11:27+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