Generated summary
PXD071171 is a DDA label-free dataset (Mus musculus) with 20 runs, 20 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 662,717 PSMs, 79,897 peptidoforms and 7,785 protein groups, and the repository holds 56,740 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 662717 where the producer reported 662825 (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 662717 where the producer reported 662825 (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 197508 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2053 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 197508 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 2053 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: 2241 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: 2241 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: 3 identifier(s), 8 row(s) dropped, e.g. PXD071171:A0A088MLT8;P0DPB4 written 2 times; quant_values: 66 identifier(s), 190 row(s) dropped, e.g. PXD071171:20181113_Q1_AWH_ColID_726_ProjID_1496_Benzing_sample_10:label_free:protein_group:PXD071171:A0A088MLT8;P0DPB4: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: 3 identifier(s), 8 row(s) dropped, e.g. PXD071171:A0A088MLT8;P0DPB4 written 2 times; quant_values: 66 identifier(s), 190 row(s) dropped, e.g. PXD071171:20181113_Q1_AWH_ColID_726_ProjID_1496_Benzing_sample_10:label_free:protein_group:PXD071171:A0A088MLT8;P0DPB4:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
51 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
51 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 | 662,717 |
| Peptidoforms at 1% FDR | 79,897 |
| Protein groups at 1% FDR | 7,785 |
| PTM sites | 56,740 |
| Quantitative values | 748,368 |
| PSMs, all (including decoys and sub-threshold) | 1,736,095 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 36.2% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 1.3% |
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
- phospho
- Instrument vendor
- not recorded
- Runs / samples
- 20 / 20
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 9df4ce025f23
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 11,859 |
| Oxidation on M | UNIMOD:35 | 9,312 |
| Deamidation on N | UNIMOD:7 | 4,907 |
| Deamidation on Q | UNIMOD:7 | 4,662 |
| Phosphoserine on S | UNIMOD:21 | 4,141 |
| Phosphorylation on S | UNIMOD:21 | 3,907 |
| Hydroxylation on P | UNIMOD:35 | 1,857 |
| Citrullination on R | UNIMOD:7 | 1,505 |
| Fe[III] on E | UNIMOD:1870 | 1,074 |
| Phosphorylation on T | UNIMOD:21 | 1,060 |
| Hydroxylation on N | UNIMOD:35 | 1,047 |
| Fe[III] on D | UNIMOD:1870 | 917 |
| Ammonia loss on N | UNIMOD:385 | 819 |
| Trimethylation on K | UNIMOD:37 | 737 |
| Fe[II] on E | UNIMOD:952 | 550 |
| Fe[II] on D | UNIMOD:952 | 503 |
| Sodium on E | UNIMOD:30 | 491 |
| Magnesium on E | UNIMOD:956 | 487 |
| Sodium on D | UNIMOD:30 | 452 |
| Hydroxylation on K | UNIMOD:35 | 446 |
| Magnesium on D | UNIMOD:956 | 420 |
| Phosphothreonine on T | UNIMOD:21 | 408 |
| Methylation on R | UNIMOD:34 | 287 |
| Calcium on E | UNIMOD:951 | 280 |
| Calcium on D | UNIMOD:951 | 279 |
| Ammonia loss on C | UNIMOD:385 | 261 |
| Carbamyl on X | UNIMOD:5 | 243 |
| Water Loss on E | UNIMOD:27 | 239 |
| Methylation on K | UNIMOD:34 | 203 |
| Phosphorylation on Y | UNIMOD:21 | 182 |
| Sulfonation on Y | UNIMOD:40 | 165 |
| Carbamyl on M | UNIMOD:5 | 161 |
| Acetylation on K | UNIMOD:1 | 146 |
| Potassium on E | UNIMOD:530 | 136 |
| Dimethylation on R | UNIMOD:36 | 132 |
| N6-acetyllysine on K | UNIMOD:1 | 126 |
| Carboxylation on E | UNIMOD:299 | 125 |
| Potassium on D | UNIMOD:530 | 117 |
| Dimethylation on K | UNIMOD:36 | 101 |
| Nitrosylation on Y | UNIMOD:354 | 96 |
| Acetylation on X | UNIMOD:1 | 90 |
| N-acetylalanine on A | UNIMOD:1 | 82 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 72 |
| Carbamyl on K | UNIMOD:5 | 69 |
| Carboxylation on D | UNIMOD:299 | 58 |
| HexNAc on S | UNIMOD:43 | 56 |
| Formylation on K | UNIMOD:122 | 50 |
| HexNAc on T | UNIMOD:43 | 47 |
| Omega-N-methylarginine on R | UNIMOD:34 | 42 |
| N-acetylserine on S | UNIMOD:1 | 41 |
| Carboxylation on K | UNIMOD:299 | 37 |
| Phosphotyrosine on Y | UNIMOD:21 | 36 |
| 4-hydroxyproline on P | UNIMOD:35 | 35 |
| Cu[I] on E | UNIMOD:531 | 33 |
| Cu[I] on D | UNIMOD:531 | 32 |
| Carbamyl on R | UNIMOD:5 | 31 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 29 |
| Carbamyl on C | UNIMOD:5 | 29 |
| Glutarylation on K | UNIMOD:1848 | 29 |
| N-acetylmethionine on M | UNIMOD:1 | 26 |
| Butyrylation on K | UNIMOD:1289 | 23 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 23 |
| N6-methyllysine on K | UNIMOD:34 | 23 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 21 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 21 |
| N6-succinyllysine on K | — | 21 |
| Crotonylation on K | UNIMOD:1363 | 20 |
| Malonylation on K | UNIMOD:747 | 20 |
| Succinylation on K | UNIMOD:64 | 19 |
| Zinc on D | UNIMOD:954 | 16 |
| Zinc on E | UNIMOD:954 | 16 |
| N5-methylglutamine on Q | UNIMOD:34 | 14 |
| N6-glutaryllysine on K | — | 14 |
| Nitrosylation on C | UNIMOD:275 | 14 |
| Hydroxybutyrylation on K | — | 13 |
| Pyridoxal phosphate on K | UNIMOD:46 | 10 |
| N-myristoyl glycine on G | UNIMOD:45 | 9 |
| ADP-ribosylation on S | UNIMOD:213 | 7 |
| N-acetylthreonine on T | UNIMOD:1 | 7 |
| N6-methacryllysine on K | — | 7 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| HexNAc on Nxt | UNIMOD:43 | 6 |
| N6-butyryllysine on K | UNIMOD:1289 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 5 |
| Tele-methylhistidine on H | UNIMOD:34 | 5 |
| Dimethylated arginine on R | UNIMOD:36 | 4 |
| HexNAc on Nxs | UNIMOD:43 | 4 |
| N-acetylglycine on G | UNIMOD:1 | 4 |
| N6-crotonyllysine on K | — | 4 |
| N-acetylvaline on V | UNIMOD:1 | 3 |
| N6-malonyllysine on K | — | 3 |
| (3R)-3-hydroxyasparagine on N | UNIMOD:35 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| N,N,N-trimethylglycine on G | — | 2 |
| S-geranylgeranyl cysteine on C | UNIMOD:48 | 2 |
| (3S)-3-hydroxylysine on K | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| 3-hydroxyproline on P | UNIMOD:35 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylcysteine on C | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-acetylproline on P | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 1 |
| O-palmitoleoyl serine on S | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 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
dfd5f024c31eb888, written 2026-10-29T12:17:19+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