Generated summary
PXD035412 is a DDA label-free dataset (Homo sapiens) with 30 runs, 30 samples and enrichment: phospho. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 1,268,270 PSMs, 76,470 peptidoforms and 6,955 protein groups, and the repository holds 64,817 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 76470 where the producer reported 76469 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
The bundle holds 76470 where the producer reported 76469 (results.txt: All target peptides with q-value <= 0.01). Both numbers are kept; treat the producer's as canonical until the difference is explained.
count_mismatch warning
The bundle holds 1.26827e+06 where the producer reported 1.26924e+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 1.26827e+06 where the producer reported 1.26924e+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 453963 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12 duplicate entry for one site and run (identical values; same protein group); 13285 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 453963 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 12 duplicate entry for one site and run (identical values; same protein group); 13285 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: 7535 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: 7535 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: 2 identifier(s), 5 row(s) dropped, e.g. PXD035412:Q3SYB3;Q5VV16;Q6VB84;Q8WXT5 written 4 times; quant_values: 60 identifier(s), 150 row(s) dropped, e.g. PXD035412:YP202127387-GM-0-1:label_free:protein_group:PXD035412:Q3SYB3;Q5VV16;Q6VB84;Q8WXT5:QuantProject:DEF-PROT-SPC written 4 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: 2 identifier(s), 5 row(s) dropped, e.g. PXD035412:Q3SYB3;Q5VV16;Q6VB84;Q8WXT5 written 4 times; quant_values: 60 identifier(s), 150 row(s) dropped, e.g. PXD035412:YP202127387-GM-0-1:label_free:protein_group:PXD035412:Q3SYB3;Q5VV16;Q6VB84;Q8WXT5:QuantProject:DEF-PROT-SPC written 4 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
344 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
344 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 | 1,268,270 |
| Peptidoforms at 1% FDR | 76,470 |
| Protein groups at 1% FDR | 6,955 |
| PTM sites | 64,817 |
| Quantitative values | 1,059,555 |
| PSMs, all (including decoys and sub-threshold) | 3,317,351 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 64.3% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.9% |
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
- phospho
- Instrument vendor
- not recorded
- Runs / samples
- 30 / 30
- Sample metadata
- absent
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v4.xml
- Pipeline commit
- 852cea5e1cd7
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Carbamidomethyl on C | UNIMOD:4 | 12,871 |
| Phosphoserine on S | UNIMOD:21 | 8,454 |
| Phosphorylation on S | UNIMOD:21 | 7,900 |
| Deamidation on N | UNIMOD:7 | 5,535 |
| Deamidation on Q | UNIMOD:7 | 4,776 |
| Phosphorylation on T | UNIMOD:21 | 3,746 |
| Oxidation on M | UNIMOD:35 | 2,829 |
| Phosphothreonine on T | UNIMOD:21 | 1,346 |
| Hydroxylation on P | UNIMOD:35 | 1,316 |
| Citrullination on R | UNIMOD:7 | 1,314 |
| Sulfonation on Y | UNIMOD:40 | 837 |
| Ammonia loss on N | UNIMOD:385 | 785 |
| Phosphorylation on Y | UNIMOD:21 | 785 |
| Carbamyl on X | UNIMOD:5 | 705 |
| Carbamyl on K | UNIMOD:5 | 668 |
| Calcium on E | UNIMOD:951 | 587 |
| Hydroxylation on N | UNIMOD:35 | 422 |
| Magnesium on E | UNIMOD:956 | 404 |
| Sodium on E | UNIMOD:30 | 404 |
| Acetylation on K | UNIMOD:1 | 403 |
| Carbamyl on M | UNIMOD:5 | 393 |
| N-acetylalanine on A | UNIMOD:1 | 390 |
| Calcium on D | UNIMOD:951 | 382 |
| Potassium on E | UNIMOD:530 | 332 |
| Methylation on K | UNIMOD:34 | 328 |
| Carboxylation on E | UNIMOD:299 | 304 |
| Ammonia loss on C | UNIMOD:385 | 290 |
| Cu[I] on E | UNIMOD:531 | 284 |
| Magnesium on D | UNIMOD:956 | 275 |
| Water Loss on E | UNIMOD:27 | 258 |
| Sodium on D | UNIMOD:30 | 256 |
| Trimethylation on K | UNIMOD:37 | 220 |
| Carboxylation on D | UNIMOD:299 | 218 |
| Potassium on D | UNIMOD:530 | 203 |
| Hydroxylation on K | UNIMOD:35 | 194 |
| Succinylation on K | UNIMOD:64 | 189 |
| Methylation on R | UNIMOD:34 | 180 |
| Cu[I] on D | UNIMOD:531 | 172 |
| N-acetylmethionine on M | UNIMOD:1 | 160 |
| Dimethylation on K | UNIMOD:36 | 153 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 151 |
| Glutarylation on K | UNIMOD:1848 | 149 |
| N-acetylserine on S | UNIMOD:1 | 148 |
| Formylation on K | UNIMOD:122 | 147 |
| Fe[III] on E | UNIMOD:1870 | 141 |
| N6-acetyllysine on K | UNIMOD:1 | 131 |
| Fe[II] on E | UNIMOD:952 | 125 |
| Acetylation on X | UNIMOD:1 | 111 |
| Dimethylation on R | UNIMOD:36 | 107 |
| Carbamyl on R | UNIMOD:5 | 103 |
| Fe[II] on D | UNIMOD:952 | 96 |
| Carboxylation on K | UNIMOD:299 | 95 |
| Phosphotyrosine on Y | UNIMOD:21 | 89 |
| Malonylation on K | UNIMOD:747 | 83 |
| Fe[III] on D | UNIMOD:1870 | 75 |
| Omega-N-methylarginine on R | UNIMOD:34 | 69 |
| Hydroxybutyrylation on K | — | 68 |
| HexNAc on S | UNIMOD:43 | 67 |
| Carbamyl on C | UNIMOD:5 | 66 |
| Crotonylation on K | UNIMOD:1363 | 58 |
| Zinc on E | UNIMOD:954 | 55 |
| Nitrosylation on Y | UNIMOD:354 | 50 |
| Butyrylation on K | UNIMOD:1289 | 48 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 41 |
| HexNAc on T | UNIMOD:43 | 40 |
| Pyridoxal phosphate on K | UNIMOD:46 | 38 |
| 4-hydroxyproline on P | UNIMOD:35 | 35 |
| Nitrosylation on C | UNIMOD:275 | 33 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 32 |
| Zinc on D | UNIMOD:954 | 30 |
| N6-methyllysine on K | UNIMOD:34 | 29 |
| N-acetylthreonine on T | UNIMOD:1 | 24 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 21 |
| Deamidated asparagine on N | UNIMOD:7 | 15 |
| ADP-ribosylation on S | UNIMOD:213 | 13 |
| N6-succinyllysine on K | — | 11 |
| Dimethylated arginine on R | UNIMOD:36 | 10 |
| N-acetylglycine on G | UNIMOD:1 | 9 |
| N6-glutaryllysine on K | — | 7 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 6 |
| N-acetylvaline on V | UNIMOD:1 | 5 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 5 |
| N-acetylcysteine on C | UNIMOD:1 | 4 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| 5-hydroxylysine on K | UNIMOD:35 | 3 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 3 |
| N,N,N-trimethylglycine on G | — | 3 |
| N6-methacryllysine on K | — | 3 |
| N6-propionyllysine on K | UNIMOD:58 | 3 |
| Pros-methylhistidine on H | UNIMOD:34 | 3 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 3 |
| 3'-nitrotyrosine on Y | — | 2 |
| 4-carboxyglutamate on E | UNIMOD:299 | 2 |
| HexNAc on Nxs | UNIMOD:43 | 2 |
| Hydroxyproline on P | UNIMOD:35 | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| (3S)-3-hydroxyhistidine on H | — | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| ADP-ribosyl glutamic acid on E | — | 1 |
| Allysine on K | UNIMOD:352 | 1 |
| Citrulline on R | UNIMOD:7 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Diphosphoserine on S | UNIMOD:898 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hypusine on K | UNIMOD:379 | 1 |
| Leucine methyl ester on L | UNIMOD:34 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N-myristoyl glycine on G | UNIMOD:45 | 1 |
| N6-crotonyllysine on K | — | 1 |
| S-farnesyl cysteine on C | UNIMOD:44 | 1 |
| Sulfotyrosine on Y | UNIMOD:40 | 1 |
| Tele-8alpha-FAD histidine on H | 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
56abdb887208651b, written 2026-10-29T10:42:59+00:00 by ingester 1.4.0- Reconciliation
- failed: psms_target_1pct, peptidoforms_target_1pct (the bundle disagrees with the producer's own count here)
- Licence
- CC-BY-4.0
- Credit
- NCEMS Aging Proteome Working Group