Generated summary
PXD049957 is a DDA label-free dataset (Mus musculus) with 34 runs, 34 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,864,731 PSMs, 82,701 peptidoforms and 7,308 protein groups, and the repository holds 55,541 PTM sites for it. 5 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, 5 warnings and 2 for information
count_mismatch warning
The bundle holds 1.86473e+06 where the producer reported 1.86494e+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 1.86473e+06 where the producer reported 1.86494e+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
15.62 avg cores of 32 allowed (S5)
15.62 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 562159 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 28 duplicate entry for one site and run (identical values; same protein group); 11156 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 562159 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 28 duplicate entry for one site and run (identical values; same protein group); 11156 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: 4552 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: 4552 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: 5 identifier(s), 8 row(s) dropped, e.g. PXD049957:A0ABA7IW16;A0ABA7IW20;A0ABA7IW39;A0ABA7IXB9;A0ABA7IXC1;A0ABA7IXC2;A0ABA7IXE7 written 3 times; quant_values: 176 identifier(s), 278 row(s) dropped, e.g. PXD049957:20231122_SiHe_0254_Set2_Phopho_sample_54:label_free:protein_group:PXD049957:A0ABA7IW16;A0ABA7IW20;A0ABA7IW39;A0ABA7IXB9;A0ABA7IXC1;A0ABA7IXC2;A0ABA7IXE7: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: 5 identifier(s), 8 row(s) dropped, e.g. PXD049957:A0ABA7IW16;A0ABA7IW20;A0ABA7IW39;A0ABA7IXB9;A0ABA7IXC1;A0ABA7IXC2;A0ABA7IXE7 written 3 times; quant_values: 176 identifier(s), 278 row(s) dropped, e.g. PXD049957:20231122_SiHe_0254_Set2_Phopho_sample_54:label_free:protein_group:PXD049957:A0ABA7IW16;A0ABA7IW20;A0ABA7IW39;A0ABA7IXB9;A0ABA7IXC1;A0ABA7IXC2;A0ABA7IXE7:QuantProject:DEF-PROT-SPC written 3 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
2380 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
2380 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 | 1,864,731 |
| Peptidoforms at 1% FDR | 82,701 |
| Protein groups at 1% FDR | 7,308 |
| PTM sites | 55,541 |
| Quantitative values | 1,305,540 |
| PSMs, all (including decoys and sub-threshold) | 3,272,476 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 59.5% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.7% |
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
- 34 / 34
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 0095bcefc3f5
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Phosphorylation on S | UNIMOD:21 | 9,831 |
| Carbamidomethyl on C | UNIMOD:4 | 9,301 |
| Phosphoserine on S | UNIMOD:21 | 8,644 |
| Oxidation on M | UNIMOD:35 | 6,031 |
| Deamidation on N | UNIMOD:7 | 3,806 |
| Phosphorylation on T | UNIMOD:21 | 2,624 |
| Deamidation on Q | UNIMOD:7 | 2,074 |
| Sodium on E | UNIMOD:30 | 1,600 |
| Sodium on D | UNIMOD:30 | 1,368 |
| Phosphothreonine on T | UNIMOD:21 | 984 |
| Ammonia loss on N | UNIMOD:385 | 898 |
| Hydroxylation on P | UNIMOD:35 | 661 |
| Water Loss on E | UNIMOD:27 | 574 |
| Carbamyl on X | UNIMOD:5 | 540 |
| Phosphorylation on Y | UNIMOD:21 | 535 |
| Calcium on E | UNIMOD:951 | 437 |
| Calcium on D | UNIMOD:951 | 426 |
| Sulfonation on Y | UNIMOD:40 | 417 |
| Magnesium on E | UNIMOD:956 | 397 |
| N6-acetyllysine on K | UNIMOD:1 | 334 |
| Magnesium on D | UNIMOD:956 | 332 |
| Hydroxylation on N | UNIMOD:35 | 283 |
| Citrullination on R | UNIMOD:7 | 279 |
| Formylation on K | UNIMOD:122 | 267 |
| N-acetylalanine on A | UNIMOD:1 | 228 |
| Ammonia loss on C | UNIMOD:385 | 219 |
| Hydroxylation on K | UNIMOD:35 | 154 |
| Acetylation on X | UNIMOD:1 | 151 |
| Phosphotyrosine on Y | UNIMOD:21 | 123 |
| Potassium on E | UNIMOD:530 | 103 |
| Potassium on D | UNIMOD:530 | 101 |
| N-acetylserine on S | UNIMOD:1 | 98 |
| N-acetylmethionine on M | UNIMOD:1 | 95 |
| Acetylation on K | UNIMOD:1 | 70 |
| N6-succinyllysine on K | — | 60 |
| Fe[III] on D | UNIMOD:1870 | 53 |
| Fe[II] on D | UNIMOD:952 | 52 |
| Fe[III] on E | UNIMOD:1870 | 48 |
| Fe[II] on E | UNIMOD:952 | 46 |
| HexNAc on S | UNIMOD:43 | 44 |
| HexNAc on T | UNIMOD:43 | 37 |
| Cu[I] on D | UNIMOD:531 | 36 |
| Cu[I] on E | UNIMOD:531 | 35 |
| Pyridoxal phosphate on K | UNIMOD:46 | 33 |
| Methylation on K | UNIMOD:34 | 32 |
| Methylation on R | UNIMOD:34 | 32 |
| Omega-N-methylarginine on R | UNIMOD:34 | 29 |
| ADP-ribosylation on S | UNIMOD:213 | 26 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 22 |
| Crotonylation on K | UNIMOD:1363 | 21 |
| Carbamyl on K | UNIMOD:5 | 20 |
| Zinc on D | UNIMOD:954 | 20 |
| 4-hydroxyproline on P | UNIMOD:35 | 18 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 18 |
| N-acetylthreonine on T | UNIMOD:1 | 18 |
| N6-methyllysine on K | UNIMOD:34 | 18 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 17 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 17 |
| Zinc on E | UNIMOD:954 | 17 |
| Carboxylation on E | UNIMOD:299 | 15 |
| Dimethylation on K | UNIMOD:36 | 14 |
| Butyrylation on K | UNIMOD:1289 | 12 |
| Carbamyl on M | UNIMOD:5 | 12 |
| Dimethylation on R | UNIMOD:36 | 12 |
| Carboxylation on D | UNIMOD:299 | 9 |
| N-acetylglycine on G | UNIMOD:1 | 8 |
| Succinylation on K | UNIMOD:64 | 8 |
| Hydroxybutyrylation on K | — | 7 |
| Malonylation on K | UNIMOD:747 | 7 |
| N6-glutaryllysine on K | — | 7 |
| Trimethylation on K | UNIMOD:37 | 7 |
| Deamidated asparagine on N | UNIMOD:7 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 6 |
| Nitrosylation on Y | UNIMOD:354 | 6 |
| Carbamyl on R | UNIMOD:5 | 5 |
| HexNAc on Nxt | UNIMOD:43 | 5 |
| Pros-methylhistidine on H | UNIMOD:34 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Carboxylation on K | UNIMOD:299 | 3 |
| Dimethylated arginine on R | UNIMOD:36 | 3 |
| HexNAc on Nxs | UNIMOD:43 | 3 |
| N-acetylcysteine on C | UNIMOD:1 | 3 |
| N5-methylglutamine on Q | UNIMOD:34 | 3 |
| N6-butyryllysine on K | UNIMOD:1289 | 3 |
| Tele-8alpha-FAD histidine on H | UNIMOD:50 | 3 |
| (3R)-3-hydroxyaspartate on D | UNIMOD:35 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| Citrulline on R | UNIMOD:7 | 2 |
| Glutarylation on K | UNIMOD:1848 | 2 |
| N6-(beta-hydroxybutyryl)lysine on K | UNIMOD:1849 | 2 |
| N6-benzoyllysine on K | UNIMOD:136 | 2 |
| N6-crotonyllysine on K | — | 2 |
| N6-propionyllysine on K | UNIMOD:58 | 2 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 2 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Carbamyl on C | UNIMOD:5 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| Lysino-D-alanine (Lys) on K | — | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-malonyllysine on K | — | 1 |
| N6-methacryllysine on K | — | 1 |
| Nitrosylation on C | UNIMOD:275 | 1 |
| Pros-8alpha-FAD histidine on H | UNIMOD:50 | 1 |
| S-8alpha-FAD cysteine on C | 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
f029bca047829450, written 2026-10-29T10:50:28+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