Generated summary
PXD027318 is a DDA label-free dataset (Homo sapiens) with 18 runs, 18 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.11. At 1% FDR the search reports 378,168 PSMs, 49,399 peptidoforms and 4,478 protein groups, and the repository holds 21,704 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 3 for information
count_mismatch warning
The bundle holds 49399 where the producer reported 49394 (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 49399 where the producer reported 49394 (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 378168 where the producer reported 378182 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 378168 where the producer reported 378182 (results.txt: All target PSMs with q-value <= 0.01 (aging:DEF-PSM-1PCT v1)). Both numbers are kept; treat the producer's as canonical until the difference is explained.
no_design_file warning
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
No experimental design file, so quantification treated every raw file as its own condition. Between-group comparisons are not available for this dataset. Producer's note: FlashLFQ treated each file as its own biorep under one blank condition; no normalization; not usable for condition comparisons (owner: QuantProject projection)
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.
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: 818 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: 818 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.
upstream_provenance_changed warning
The search recorded its upstream 'db_prepare' provenance (db/provenance.json) with sha256 6c40902506a8bd4a99fe884bae6d95be46f8a1647d50570879ddcd3b3a79de59, and the file there now has 812ce696ba3f0ee2a1f79241b5e16e9267d6199f7598af77391178b825658963: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the db_prepare stage is gone unless the producer archived it.
The search recorded its upstream 'db_prepare' provenance (db/provenance.json) with sha256 6c40902506a8bd4a99fe884bae6d95be46f8a1647d50570879ddcd3b3a79de59, and the file there now has 812ce696ba3f0ee2a1f79241b5e16e9267d6199f7598af77391178b825658963: it was overwritten after the search. It is left out of this bundle rather than read as this search's record. The search's own record of the db_prepare stage is gone unless the producer archived it.
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: 1 identifier(s), 2 row(s) dropped, e.g. PXD027318:A6NJZ7;A6NNM3;Q9UFD9 written 3 times; quant_values: 18 identifier(s), 36 row(s) dropped, e.g. PXD027318:02-01-18_AD-HMEC-WCL_E-Luc_D1_02:label_free:protein_group:PXD027318:A6NJZ7;A6NNM3;Q9UFD9: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: 1 identifier(s), 2 row(s) dropped, e.g. PXD027318:A6NJZ7;A6NNM3;Q9UFD9 written 3 times; quant_values: 18 identifier(s), 36 row(s) dropped, e.g. PXD027318:02-01-18_AD-HMEC-WCL_E-Luc_D1_02:label_free:protein_group:PXD027318:A6NJZ7;A6NNM3;Q9UFD9:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
no_output_sdrf info
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
The search did not write an SDRF back out, so sample metadata comes from the deposited SDRF only. Producer's note: no reanalysis SDRF written (WriteSdrf is MetaMorpheus #2816, unreleased)
occupancy_decoy_groups info
263 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
263 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 | 378,168 |
| Peptidoforms at 1% FDR | 49,399 |
| Protein groups at 1% FDR | 4,478 |
| PTM sites | 21,704 |
| Quantitative values | 450,391 |
| PSMs, all (including decoys and sub-threshold) | 575,812 |
| MS2 identification rate (aging:DEF-ID-RATE) | 70.6% |
| Contaminant share of PSMs (aging:DEF-CONTAM-PSM) | 0.4% |
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
- 18 / 18
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.11
- Protein database
- uniprotkb_proteome_UP000005640_AND_revi_2026_09_18.xml
- Pipeline commit
- 152a5afe9cec
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 10,406 |
| Deamidation on Q | UNIMOD:7 | 2,153 |
| Deamidation on N | UNIMOD:7 | 1,974 |
| Oxidation on M | UNIMOD:35 | 1,796 |
| Carbamyl on X | UNIMOD:5 | 680 |
| Citrullination on R | UNIMOD:7 | 446 |
| Phosphoserine on S | UNIMOD:21 | 301 |
| N-acetylalanine on A | UNIMOD:1 | 279 |
| Hydroxylation on P | UNIMOD:35 | 143 |
| N-acetylmethionine on M | UNIMOD:1 | 137 |
| Ammonia loss on N | UNIMOD:385 | 134 |
| Methylation on K | UNIMOD:34 | 125 |
| N-acetylserine on S | UNIMOD:1 | 117 |
| Phosphorylation on S | UNIMOD:21 | 115 |
| Ammonia loss on C | UNIMOD:385 | 98 |
| Hydroxylation on N | UNIMOD:35 | 93 |
| Hydroxylation on K | UNIMOD:35 | 75 |
| Acetylation on K | UNIMOD:1 | 74 |
| Trimethylation on K | UNIMOD:37 | 73 |
| Acetylation on X | UNIMOD:1 | 71 |
| Carbamyl on M | UNIMOD:5 | 69 |
| Methylation on R | UNIMOD:34 | 64 |
| N6-acetyllysine on K | UNIMOD:1 | 63 |
| Carbamyl on K | UNIMOD:5 | 60 |
| Dimethylation on K | UNIMOD:36 | 56 |
| Fe[III] on D | UNIMOD:1870 | 55 |
| Fe[III] on E | UNIMOD:1870 | 51 |
| Fe[II] on D | UNIMOD:952 | 49 |
| Fe[II] on E | UNIMOD:952 | 48 |
| Omega-N-methylarginine on R | UNIMOD:34 | 45 |
| Phosphothreonine on T | UNIMOD:21 | 41 |
| Dimethylation on R | UNIMOD:36 | 36 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 33 |
| Phosphorylation on T | UNIMOD:21 | 31 |
| Carboxylation on D | UNIMOD:299 | 30 |
| N-acetylthreonine on T | UNIMOD:1 | 30 |
| Sodium on D | UNIMOD:30 | 25 |
| Carboxylation on E | UNIMOD:299 | 24 |
| Magnesium on D | UNIMOD:956 | 24 |
| Sodium on E | UNIMOD:30 | 22 |
| N6-methyllysine on K | UNIMOD:34 | 21 |
| Formylation on K | UNIMOD:122 | 20 |
| Carbamyl on C | UNIMOD:5 | 19 |
| HexNAc on S | UNIMOD:43 | 19 |
| Phosphorylation on Y | UNIMOD:21 | 18 |
| Magnesium on E | UNIMOD:956 | 17 |
| Water Loss on E | UNIMOD:27 | 17 |
| Butyrylation on K | UNIMOD:1289 | 15 |
| Sulfonation on Y | UNIMOD:40 | 15 |
| Carbamyl on R | UNIMOD:5 | 14 |
| N-myristoyl glycine on G | UNIMOD:45 | 14 |
| Carboxylation on K | UNIMOD:299 | 13 |
| Hydroxybutyrylation on K | — | 13 |
| Nitrosylation on Y | UNIMOD:354 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 11 |
| Dimethylated arginine on R | UNIMOD:36 | 11 |
| 4-hydroxyproline on P | UNIMOD:35 | 9 |
| HexNAc on T | UNIMOD:43 | 9 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 9 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 8 |
| Calcium on D | UNIMOD:951 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N6-glutaryllysine on K | — | 6 |
| Crotonylation on K | UNIMOD:1363 | 5 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| Phosphotyrosine on Y | UNIMOD:21 | 5 |
| Calcium on E | UNIMOD:951 | 4 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N5-methylglutamine on Q | UNIMOD:34 | 4 |
| N6-succinyllysine on K | — | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| HexNAc on Nxt | UNIMOD:43 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-methacryllysine on K | — | 2 |
| O-palmitoleoyl serine on S | — | 2 |
| Potassium on E | UNIMOD:530 | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carbamidomethyl on U | UNIMOD:4 | 1 |
| Diphthamide on H | UNIMOD:375 | 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-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-crotonyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| Potassium on D | UNIMOD:530 | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
4b75374ba407531d, written 2026-10-29T11:15:09+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