Generated summary
PXD044996 is a DDA label-free dataset (Mus musculus) with 25 runs, 25 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 285,043 PSMs, 37,623 peptidoforms and 4,166 protein groups, and the repository holds 17,804 PTM sites for it. 9 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, 9 warnings and 2 for information
calibration_failed warning
GPTMD/search ran on uncalibrated spectra (S7)
GPTMD/search ran on uncalibrated spectra (S7)
count_mismatch warning
The bundle holds 285043 where the producer reported 285046 (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 285043 where the producer reported 285046 (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.
high_contamination warning
10.04% of protein intensity in the worst file, 2.46% median across 25 files (DEF-QC-9 v3.5)
10.04% of protein intensity in the worst file, 2.46% median across 25 files (DEF-QC-9 v3.5)
low_core_use warning
15.4 avg cores of 32 allowed (S5)
15.4 avg cores of 32 allowed (S5)
low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 285046/2121025 = 13.44% of MS2 identified (S3)
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 285046/2121025 = 13.44% of MS2 identified (S3)
mbr_kept_exceeds_msms warning
kept MBR 429453 > MSMS 246757 (DEF-MBR-KEPT v1)
kept MBR 429453 > MSMS 246757 (DEF-MBR-KEPT v1)
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 25267 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5647 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 25267 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 5647 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: 832 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: 832 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: 1 identifier(s), 2 row(s) dropped, e.g. PXD044996:O54790;O54791;Q61827 written 3 times; quant_values: 25 identifier(s), 50 row(s) dropped, e.g. PXD044996:ApoE_03M_1:label_free:protein_group:PXD044996:O54790;O54791;Q61827: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. PXD044996:O54790;O54791;Q61827 written 3 times; quant_values: 25 identifier(s), 50 row(s) dropped, e.g. PXD044996:ApoE_03M_1:label_free:protein_group:PXD044996:O54790;O54791;Q61827:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
27 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
27 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 | 285,043 |
| Peptidoforms at 1% FDR | 37,623 |
| Protein groups at 1% FDR | 4,166 |
| PTM sites | 17,804 |
| Quantitative values | 912,080 |
| PSMs, all (including decoys and sub-threshold) | 426,678 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 13.4% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 2.2% |
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
- 25 / 25
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2eb9a52d7f0c
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 8,736 |
| Oxidation on M | UNIMOD:35 | 3,566 |
| Deamidation on N | UNIMOD:7 | 624 |
| Sodium on E | UNIMOD:30 | 446 |
| Hydroxylation on P | UNIMOD:35 | 390 |
| Sodium on D | UNIMOD:30 | 371 |
| Deamidation on Q | UNIMOD:7 | 332 |
| N-acetylalanine on A | UNIMOD:1 | 236 |
| Hydroxylation on N | UNIMOD:35 | 180 |
| Magnesium on E | UNIMOD:956 | 180 |
| Ammonia loss on C | UNIMOD:385 | 178 |
| Magnesium on D | UNIMOD:956 | 152 |
| Fe[III] on E | UNIMOD:1870 | 146 |
| Acetylation on X | UNIMOD:1 | 137 |
| Calcium on E | UNIMOD:951 | 131 |
| Calcium on D | UNIMOD:951 | 126 |
| Ammonia loss on N | UNIMOD:385 | 124 |
| Fe[III] on D | UNIMOD:1870 | 117 |
| Phosphoserine on S | UNIMOD:21 | 100 |
| Citrullination on R | UNIMOD:7 | 97 |
| Hydroxylation on K | UNIMOD:35 | 90 |
| N-acetylmethionine on M | UNIMOD:1 | 90 |
| N-acetylserine on S | UNIMOD:1 | 76 |
| Fe[II] on D | UNIMOD:952 | 73 |
| Fe[II] on E | UNIMOD:952 | 67 |
| N6-acetyllysine on K | UNIMOD:1 | 54 |
| Methylation on K | UNIMOD:34 | 51 |
| Carbamyl on X | UNIMOD:5 | 40 |
| Water Loss on E | UNIMOD:27 | 34 |
| Carbamyl on M | UNIMOD:5 | 33 |
| Potassium on E | UNIMOD:530 | 31 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 30 |
| Phosphorylation on S | UNIMOD:21 | 24 |
| Acetylation on K | UNIMOD:1 | 23 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 23 |
| N-acetylthreonine on T | UNIMOD:1 | 21 |
| Potassium on D | UNIMOD:530 | 20 |
| Methylation on R | UNIMOD:34 | 18 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 17 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 15 |
| Dimethylation on K | UNIMOD:36 | 13 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 13 |
| N6-methyllysine on K | UNIMOD:34 | 13 |
| Deamidated asparagine on N | UNIMOD:7 | 12 |
| Dimethylation on R | UNIMOD:36 | 12 |
| 4-hydroxyproline on P | UNIMOD:35 | 11 |
| Trimethylation on K | UNIMOD:37 | 11 |
| Omega-N-methylarginine on R | UNIMOD:34 | 10 |
| Phosphorylation on T | UNIMOD:21 | 10 |
| Phosphothreonine on T | UNIMOD:21 | 10 |
| HexNAc on T | UNIMOD:43 | 8 |
| Carbamyl on C | UNIMOD:5 | 7 |
| Carbamyl on K | UNIMOD:5 | 7 |
| N-acetylglycine on G | UNIMOD:1 | 7 |
| N-acetylvaline on V | UNIMOD:1 | 7 |
| HexNAc on S | UNIMOD:43 | 6 |
| Phosphorylation on Y | UNIMOD:21 | 6 |
| Formylation on K | UNIMOD:122 | 5 |
| Glutarylation on K | UNIMOD:1848 | 5 |
| Carbamyl on R | UNIMOD:5 | 4 |
| Citrulline on R | UNIMOD:7 | 4 |
| Cu[I] on E | UNIMOD:531 | 4 |
| N6-succinyllysine on K | — | 4 |
| Phosphotyrosine on Y | UNIMOD:21 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Hydroxybutyrylation on K | — | 3 |
| N-myristoyl glycine on G | UNIMOD:45 | 3 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Cu[I] on D | UNIMOD:531 | 2 |
| Dimethylated arginine on R | UNIMOD:36 | 2 |
| Leucine methyl ester on L | UNIMOD:34 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| Succinylation on K | UNIMOD:64 | 2 |
| Sulfonation on Y | UNIMOD:40 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 3'-nitrotyrosine on Y | — | 1 |
| Crotonylation on K | UNIMOD:1363 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Deamidated glutamine on Q | UNIMOD:7 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Malonylation on K | UNIMOD:747 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-benzoyllysine on K | UNIMOD:136 | 1 |
| N6-biotinyllysine on K | UNIMOD:3 | 1 |
| N6-glutaryllysine on K | — | 1 |
| Pros-methylhistidine on H | UNIMOD:34 | 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
438d6b12218fecb1, written 2026-10-29T09:17:40+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