Generated summary
PXD005123 is a DDA label-free dataset (Homo sapiens) with 20 runs, 20 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.13. At 1% FDR the search reports 1,101,243 PSMs, 86,630 peptidoforms and 7,889 protein groups, and the repository holds 25,195 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 1 for information
count_mismatch warning
The bundle holds 1.10124e+06 where the producer reported 1.10125e+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 1.10124e+06 where the producer reported 1.10125e+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.
low_core_use warning
9.47 avg cores of 32 allowed (S5)
9.47 avg cores of 32 allowed (S5)
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 133458 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 13507 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 133458 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 13507 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).
peptide_rows_localization_ambiguous warning
253 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 868 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAAAAAAAEQQSSNGPVK[Common Biological:Hydroxylation on K]K|AAAAAAAAEQQSSNGP[Common Biological:Hydroxylation on P]VKK|AAAAAAAAEQQSSN[Common Biological:Hydroxylation on N]GPVKK`, `AAEEAPEE[Metal:Fe[III] on E]APEDAAR|AAEEAPE[Metal:Fe[III] on E]EAPEDAAR`, `AAMGPGISRM[Common Variable:Oxidation on M]ND[Common Biological:Carboxylation on D]LTIIQTTQGFC[Common Fixed:Carbamidomethyl on C]R|AAM[Common Variable:Oxidation on M]GPGISRMND[Common Biological:Carboxylation on D]LTIIQTTQGFC[Common Fixed:Carbamidomethyl on C]R`.
253 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 868 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAAAAAAAEQQSSNGPVK[Common Biological:Hydroxylation on K]K|AAAAAAAAEQQSSNGP[Common Biological:Hydroxylation on P]VKK|AAAAAAAAEQQSSN[Common Biological:Hydroxylation on N]GPVKK`, `AAEEAPEE[Metal:Fe[III] on E]APEDAAR|AAEEAPE[Metal:Fe[III] on E]EAPEDAAR`, `AAMGPGISRM[Common Variable:Oxidation on M]ND[Common Biological:Carboxylation on D]LTIIQTTQGFC[Common Fixed:Carbamidomethyl on C]R|AAM[Common Variable:Oxidation on M]GPGISRMND[Common Biological:Carboxylation on D]LTIIQTTQGFC[Common Fixed:Carbamidomethyl on C]R`.
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: 2711 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: 2711 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.
occupancy_decoy_groups info
12 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
12 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 | 1,101,243 |
| Peptidoforms at 1% FDR | 86,630 |
| Protein groups at 1% FDR | 7,889 |
| PTM sites | 25,195 |
| Quantitative values | 1,034,219 |
| PSMs, all (including decoys and sub-threshold) | 1,516,532 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 98.1% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.8% |
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
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.13
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v6.xml
- Pipeline commit
- 314f6ae55a6e
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 15,442 |
| Oxidation on M | UNIMOD:35 | 2,353 |
| Carbamyl on X | UNIMOD:5 | 1,122 |
| Deamidation on N | UNIMOD:7 | 767 |
| Phosphoserine on S | UNIMOD:21 | 425 |
| N-acetylalanine on A | UNIMOD:1 | 396 |
| Ammonia loss on N | UNIMOD:385 | 306 |
| Ammonia loss on C | UNIMOD:385 | 254 |
| Acetylation on X | UNIMOD:1 | 238 |
| Fe[III] on E | UNIMOD:1870 | 228 |
| N-acetylmethionine on M | UNIMOD:1 | 226 |
| Deamidation on Q | UNIMOD:7 | 199 |
| Water Loss on E | UNIMOD:27 | 199 |
| Fe[III] on D | UNIMOD:1870 | 191 |
| Sodium on E | UNIMOD:30 | 184 |
| Hydroxylation on P | UNIMOD:35 | 155 |
| N6-acetyllysine on K | UNIMOD:1 | 152 |
| Sodium on D | UNIMOD:30 | 145 |
| N-acetylserine on S | UNIMOD:1 | 136 |
| Hydroxylation on N | UNIMOD:35 | 102 |
| Omega-N-methylarginine on R | UNIMOD:34 | 101 |
| Phosphorylation on S | UNIMOD:21 | 78 |
| Phosphothreonine on T | UNIMOD:21 | 75 |
| Phosphorylation on T | UNIMOD:21 | 71 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 67 |
| Calcium on D | UNIMOD:951 | 61 |
| Dimethylation on R | UNIMOD:36 | 60 |
| Methylation on K | UNIMOD:34 | 55 |
| Magnesium on E | UNIMOD:956 | 54 |
| Magnesium on D | UNIMOD:956 | 50 |
| Calcium on E | UNIMOD:951 | 48 |
| Fe[II] on D | UNIMOD:952 | 46 |
| Nitrosylation on Y | UNIMOD:354 | 39 |
| Methylation on R | UNIMOD:34 | 36 |
| N6-methyllysine on K | UNIMOD:34 | 34 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 32 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 29 |
| Acetylation on K | UNIMOD:1 | 27 |
| Hydroxylation on K | UNIMOD:35 | 27 |
| N-acetylthreonine on T | UNIMOD:1 | 26 |
| N-myristoyl glycine on G | UNIMOD:45 | 26 |
| N6-benzoyllysine on K | UNIMOD:136 | 24 |
| Potassium on D | UNIMOD:530 | 23 |
| Citrullination on R | UNIMOD:7 | 22 |
| HexNAc on S | UNIMOD:43 | 22 |
| Potassium on E | UNIMOD:530 | 21 |
| HexNAc on T | UNIMOD:43 | 19 |
| Deamidated asparagine on N | UNIMOD:7 | 17 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 16 |
| Phosphotyrosine on Y | UNIMOD:21 | 16 |
| Fe[II] on E | UNIMOD:952 | 15 |
| Dimethylation on K | UNIMOD:36 | 14 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 14 |
| Phosphorylation on Y | UNIMOD:21 | 14 |
| N6-succinyllysine on K | — | 13 |
| Carbamyl on M | UNIMOD:5 | 12 |
| Glutarylation on K | UNIMOD:1848 | 12 |
| Malonylation on K | UNIMOD:747 | 12 |
| Trimethylation on K | UNIMOD:37 | 12 |
| Dimethylated arginine on R | UNIMOD:36 | 11 |
| N6-butyryllysine on K | UNIMOD:1289 | 11 |
| 4-hydroxyproline on P | UNIMOD:35 | 10 |
| Formylation on K | UNIMOD:122 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 10 |
| N6-crotonyllysine on K | — | 10 |
| Citrulline on R | UNIMOD:7 | 9 |
| Carbamyl on K | UNIMOD:5 | 8 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 8 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 8 |
| Carbamyl on R | UNIMOD:5 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 7 |
| Zinc on D | UNIMOD:954 | 7 |
| 3'-nitrotyrosine on Y | — | 6 |
| Allysine on K | UNIMOD:352 | 5 |
| Butyrylation on K | UNIMOD:1289 | 5 |
| Succinylation on K | UNIMOD:64 | 5 |
| Hydroxybutyrylation on K | — | 4 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carboxylation on D | UNIMOD:299 | 3 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| S-farnesyl cysteine on C | UNIMOD:44 | 3 |
| S-nitrosocysteine on C | UNIMOD:275 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| (3S)-3-hydroxylysine on K | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Carbamyl on C | UNIMOD:5 | 2 |
| Carboxylation on E | UNIMOD:299 | 2 |
| Crotonylation on K | UNIMOD:1363 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| N5-methylglutamine on Q | UNIMOD:34 | 2 |
| N6-acetyl-N6-methyllysine on K | — | 2 |
| N6-glutaryllysine on K | — | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| Sulfonation on Y | UNIMOD:40 | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carboxylation on K | UNIMOD:299 | 1 |
| Cu[I] on E | UNIMOD:531 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| HexNAc on Nxt | UNIMOD:43 | 1 |
| Hypusine on K | UNIMOD:379 | 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-propionyllysine on K | UNIMOD:58 | 1 |
| S-(15-deoxy-Delta12,14-prostaglandin J2-9-yl)cysteine on C | — | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
7872bc32a7efe7f6, written 2026-10-31T11:51:35+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