Generated summary
PXD014098 is a DDA label-free dataset (Mus musculus) with 16 runs, 16 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,040,626 PSMs, 73,647 peptidoforms and 4,933 protein groups, and the repository holds 32,132 PTM sites for it. 4 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, 4 warnings and 2 for information
count_mismatch warning
The bundle holds 1.04063e+06 where the producer reported 1.04066e+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 1.04063e+06 where the producer reported 1.04066e+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 141239 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 7593 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 141239 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 4 duplicate entry for one site and run (identical values; same protein group); 7593 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).
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: 2834 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: 2834 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: 8 identifier(s), 9 row(s) dropped, e.g. PXD014098:A0A087WR13;A0A571BD48 written 2 times; quant_values: 133 identifier(s), 149 row(s) dropped, e.g. PXD014098:20190310_CT_ColID_796_Marie_Rurgali_mouse_hepatocytes_insol_KO1_2hstrv:label_free:protein_group:PXD014098:A0A087WR13;A0A571BD48:QuantProject:DEF-PROT-INT 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: 8 identifier(s), 9 row(s) dropped, e.g. PXD014098:A0A087WR13;A0A571BD48 written 2 times; quant_values: 133 identifier(s), 149 row(s) dropped, e.g. PXD014098:20190310_CT_ColID_796_Marie_Rurgali_mouse_hepatocytes_insol_KO1_2hstrv:label_free:protein_group:PXD014098:A0A087WR13;A0A571BD48:QuantProject:DEF-PROT-INT written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
100 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
100 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 | 1,040,626 |
| Peptidoforms at 1% FDR | 73,647 |
| Protein groups at 1% FDR | 4,933 |
| PTM sites | 32,132 |
| Quantitative values | 720,624 |
| PSMs, all (including decoys and sub-threshold) | 1,522,216 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 74.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.2% |
How it was measured
- Organism searched
- Mus musculus (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
- 16 / 16
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 5aec9eb024d8
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 7,950 |
| Oxidation on M | UNIMOD:35 | 5,218 |
| Deamidation on Q | UNIMOD:7 | 3,713 |
| Deamidation on N | UNIMOD:7 | 3,119 |
| Hydroxylation on P | UNIMOD:35 | 1,211 |
| Citrullination on R | UNIMOD:7 | 979 |
| Ammonia loss on N | UNIMOD:385 | 714 |
| Hydroxylation on N | UNIMOD:35 | 589 |
| Carbamyl on X | UNIMOD:5 | 511 |
| Sodium on E | UNIMOD:30 | 456 |
| N6-acetyllysine on K | UNIMOD:1 | 389 |
| Fe[III] on E | UNIMOD:1870 | 381 |
| Sodium on D | UNIMOD:30 | 373 |
| Hydroxylation on K | UNIMOD:35 | 356 |
| Fe[III] on D | UNIMOD:1870 | 304 |
| Phosphoserine on S | UNIMOD:21 | 283 |
| Methylation on K | UNIMOD:34 | 266 |
| Water Loss on E | UNIMOD:27 | 257 |
| Magnesium on E | UNIMOD:956 | 253 |
| Formylation on K | UNIMOD:122 | 239 |
| N-acetylalanine on A | UNIMOD:1 | 238 |
| Magnesium on D | UNIMOD:956 | 233 |
| Ammonia loss on C | UNIMOD:385 | 216 |
| Acetylation on X | UNIMOD:1 | 203 |
| Phosphorylation on T | UNIMOD:21 | 195 |
| Phosphorylation on S | UNIMOD:21 | 191 |
| Methylation on R | UNIMOD:34 | 139 |
| Calcium on E | UNIMOD:951 | 135 |
| Acetylation on K | UNIMOD:1 | 131 |
| Calcium on D | UNIMOD:951 | 109 |
| N-acetylmethionine on M | UNIMOD:1 | 108 |
| N-acetylserine on S | UNIMOD:1 | 97 |
| N6-succinyllysine on K | — | 95 |
| Carbamyl on K | UNIMOD:5 | 93 |
| Fe[II] on E | UNIMOD:952 | 86 |
| Fe[II] on D | UNIMOD:952 | 80 |
| Dimethylation on K | UNIMOD:36 | 75 |
| Sulfonation on Y | UNIMOD:40 | 67 |
| HexNAc on S | UNIMOD:43 | 64 |
| Potassium on E | UNIMOD:530 | 60 |
| HexNAc on T | UNIMOD:43 | 58 |
| Crotonylation on K | UNIMOD:1363 | 57 |
| Trimethylation on K | UNIMOD:37 | 57 |
| Dimethylation on R | UNIMOD:36 | 55 |
| Nitrosylation on Y | UNIMOD:354 | 55 |
| Phosphothreonine on T | UNIMOD:21 | 55 |
| Potassium on D | UNIMOD:530 | 53 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 52 |
| Phosphorylation on Y | UNIMOD:21 | 51 |
| Carboxylation on E | UNIMOD:299 | 45 |
| Butyrylation on K | UNIMOD:1289 | 40 |
| Succinylation on K | UNIMOD:64 | 34 |
| Carbamyl on R | UNIMOD:5 | 29 |
| Glutarylation on K | UNIMOD:1848 | 28 |
| Malonylation on K | UNIMOD:747 | 28 |
| Carbamyl on M | UNIMOD:5 | 22 |
| Cu[I] on E | UNIMOD:531 | 22 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 22 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 22 |
| N6-methyllysine on K | UNIMOD:34 | 22 |
| 4-hydroxyproline on P | UNIMOD:35 | 21 |
| Pyridoxal phosphate on K | UNIMOD:46 | 20 |
| Carboxylation on D | UNIMOD:299 | 18 |
| Hydroxybutyrylation on K | — | 18 |
| N-acetylthreonine on T | UNIMOD:1 | 18 |
| Carboxylation on K | UNIMOD:299 | 16 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 16 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 15 |
| Carbamyl on C | UNIMOD:5 | 15 |
| Omega-N-methylarginine on R | UNIMOD:34 | 15 |
| Nitrosylation on C | UNIMOD:275 | 14 |
| N6-glutaryllysine on K | — | 13 |
| Cu[I] on D | UNIMOD:531 | 11 |
| HexNAc on Nxt | UNIMOD:43 | 11 |
| Phosphotyrosine on Y | UNIMOD:21 | 11 |
| Deamidated asparagine on N | UNIMOD:7 | 10 |
| N-myristoyl glycine on G | UNIMOD:45 | 8 |
| Pros-methylhistidine on H | UNIMOD:34 | 8 |
| Citrulline on R | UNIMOD:7 | 7 |
| N6-methacryllysine on K | — | 7 |
| Allysine on K | UNIMOD:352 | 6 |
| N-acetylglycine on G | UNIMOD:1 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 6 |
| Zinc on E | UNIMOD:954 | 6 |
| 3'-nitrotyrosine on Y | — | 5 |
| N5-methylglutamine on Q | UNIMOD:34 | 5 |
| N6-crotonyllysine on K | — | 5 |
| N6-malonyllysine on K | — | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-glutamyl serotonin on Q | — | 3 |
| N6-benzoyllysine on K | UNIMOD:136 | 3 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 3 |
| Zinc on D | UNIMOD:954 | 3 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-lipoyllysine on K | UNIMOD:42 | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| (3S)-3-hydroxyasparagine on N | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| HexNAc on Nxs | UNIMOD:43 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-(pyridoxal phosphate)lysine on K | UNIMOD:46 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-butyryllysine on K | UNIMOD:1289 | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| O-AMP-threonine on T | UNIMOD:405 | 1 |
| Pros-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| S-(2,3-dicarboxypropyl)cysteine on C | — | 1 |
| S-nitrosocysteine on C | UNIMOD:275 | 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
a1df809076997655, written 2026-10-29T12:20:48+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