Generated summary
PXD008344 is a DDA label-free dataset (Homo sapiens) with 44 runs, 44 samples and no enrichment step (whole proteome). It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 766,417 PSMs, 150,696 peptidoforms and 8,640 protein groups, and the repository holds 61,855 PTM sites for it. 6 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, 6 warnings and 2 for information
count_mismatch warning
The bundle holds 150696 where the producer reported 150695 (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 150696 where the producer reported 150695 (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 766417 where the producer reported 766601 (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 766417 where the producer reported 766601 (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
7.02% of protein intensity in the worst file, 0.18% median across 44 files (DEF-QC-9 v3.5)
7.02% of protein intensity in the worst file, 0.18% median across 44 files (DEF-QC-9 v3.5)
occupancy_not_stored warning
Of 141571 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7799 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 141571 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 7799 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).
sdrf_uncoded warning
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: disease: multiple sclerosis; organism part: brain. Match on it as text; it has not been mapped to a term.
The deposited SDRF describes its samples only as text with no ontology term, so the curated organism part, cell type, disease and individual columns are empty. The text is in sample_characteristics: disease: multiple sclerosis; organism part: brain. Match on it as text; it has not been mapped to a term.
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: 3002 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: 3002 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: 6 identifier(s), 8 row(s) dropped, e.g. PXD008344:A0AAG2TJA1;Q9UF83 written 2 times; quant_values: 265 identifier(s), 353 row(s) dropped, e.g. PXD008344:20160312_02_A1:label_free:protein_group:PXD008344:A0AAG2TJA1;Q9UF83: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: 6 identifier(s), 8 row(s) dropped, e.g. PXD008344:A0AAG2TJA1;Q9UF83 written 2 times; quant_values: 265 identifier(s), 353 row(s) dropped, e.g. PXD008344:20160312_02_A1:label_free:protein_group:PXD008344:A0AAG2TJA1;Q9UF83:QuantProject:DEF-PROT-SPC written 2 times. The full list is in bundle.json under collapsed_duplicates.
occupancy_decoy_groups info
81 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.
81 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 | 766,417 |
| Peptidoforms at 1% FDR | 150,696 |
| Protein groups at 1% FDR | 8,640 |
| PTM sites | 61,855 |
| Quantitative values | 1,035,611 |
| PSMs, all (including decoys and sub-threshold) | 1,522,827 |
| MS2 identification rate (pxreprise:DEF-ID-RATE) | 57.8% |
| Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM) | 0.2% |
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
- none
- Instrument vendor
- Thermo
- Runs / samples
- 44 / 44
- Sample metadata
- trusted
- Search engine
- MetaMorpheus 1.1.12
- Protein database
- UP000005640_all_genecentric_2026_03_agingPTM-v3.xml
- Pipeline commit
- 2eb9a52d7f0c
Modifications
| Search engine's name | UNIMOD | Sites |
|---|---|---|
| Oxidation on M | UNIMOD:35 | 11,380 |
| Carbamidomethyl on C | UNIMOD:4 | 7,912 |
| Deamidation on N | UNIMOD:7 | 6,242 |
| Deamidation on Q | UNIMOD:7 | 4,317 |
| Fe[III] on E | UNIMOD:1870 | 2,763 |
| Hydroxylation on P | UNIMOD:35 | 2,298 |
| Fe[III] on D | UNIMOD:1870 | 2,248 |
| Citrullination on R | UNIMOD:7 | 2,057 |
| Fe[II] on E | UNIMOD:952 | 1,500 |
| Carbamyl on X | UNIMOD:5 | 1,465 |
| Ammonia loss on N | UNIMOD:385 | 1,380 |
| Fe[II] on D | UNIMOD:952 | 1,304 |
| Hydroxylation on N | UNIMOD:35 | 1,252 |
| Sodium on E | UNIMOD:30 | 891 |
| Phosphoserine on S | UNIMOD:21 | 714 |
| Magnesium on E | UNIMOD:956 | 712 |
| Calcium on E | UNIMOD:951 | 707 |
| Sodium on D | UNIMOD:30 | 705 |
| Carbamyl on M | UNIMOD:5 | 654 |
| Calcium on D | UNIMOD:951 | 612 |
| Acetylation on K | UNIMOD:1 | 581 |
| Magnesium on D | UNIMOD:956 | 544 |
| Methylation on R | UNIMOD:34 | 514 |
| Methylation on K | UNIMOD:34 | 505 |
| Phosphorylation on S | UNIMOD:21 | 492 |
| N-acetylalanine on A | UNIMOD:1 | 463 |
| Water Loss on E | UNIMOD:27 | 457 |
| Hydroxylation on K | UNIMOD:35 | 421 |
| Acetylation on X | UNIMOD:1 | 398 |
| Phosphorylation on T | UNIMOD:21 | 297 |
| Trimethylation on K | UNIMOD:37 | 280 |
| N6-acetyllysine on K | UNIMOD:1 | 257 |
| Formylation on K | UNIMOD:122 | 242 |
| Dimethylation on R | UNIMOD:36 | 231 |
| N-acetylmethionine on M | UNIMOD:1 | 216 |
| Carbamyl on K | UNIMOD:5 | 203 |
| Carboxylation on E | UNIMOD:299 | 202 |
| Nitrosylation on Y | UNIMOD:354 | 200 |
| Ammonia loss on C | UNIMOD:385 | 197 |
| HexNAc on S | UNIMOD:43 | 196 |
| HexNAc on T | UNIMOD:43 | 196 |
| GG (Ubiquitination Site) on K | UNIMOD:121 | 192 |
| Potassium on E | UNIMOD:530 | 186 |
| Glutarylation on K | UNIMOD:1848 | 178 |
| N-acetylserine on S | UNIMOD:1 | 178 |
| Carboxylation on D | UNIMOD:299 | 172 |
| Potassium on D | UNIMOD:530 | 170 |
| Dimethylation on K | UNIMOD:36 | 163 |
| Phosphothreonine on T | UNIMOD:21 | 153 |
| Carbamyl on R | UNIMOD:5 | 146 |
| Succinylation on K | UNIMOD:64 | 124 |
| 4-hydroxyproline on P | UNIMOD:35 | 98 |
| Omega-N-methylarginine on R | UNIMOD:34 | 94 |
| Cu[I] on E | UNIMOD:531 | 78 |
| Hydroxybutyrylation on K | — | 76 |
| N6-succinyllysine on K | — | 76 |
| Phosphorylation on Y | UNIMOD:21 | 68 |
| Crotonylation on K | UNIMOD:1363 | 67 |
| Sulfonation on Y | UNIMOD:40 | 60 |
| Cu[I] on D | UNIMOD:531 | 59 |
| Pyridoxal phosphate on K | UNIMOD:46 | 59 |
| Asymmetric dimethylarginine on R | UNIMOD:36 | 52 |
| Malonylation on K | UNIMOD:747 | 49 |
| Carboxylation on K | UNIMOD:299 | 45 |
| N-acetylthreonine on T | UNIMOD:1 | 41 |
| Carbamyl on C | UNIMOD:5 | 40 |
| Butyrylation on K | UNIMOD:1289 | 39 |
| N6-methyllysine on K | UNIMOD:34 | 39 |
| Nitrosylation on C | UNIMOD:275 | 36 |
| N6,N6,N6-trimethyllysine on K | UNIMOD:37 | 30 |
| Phosphotyrosine on Y | UNIMOD:21 | 25 |
| Citrulline on R | UNIMOD:7 | 23 |
| N-myristoyl glycine on G | UNIMOD:45 | 21 |
| Zinc on D | UNIMOD:954 | 20 |
| N6,N6-dimethyllysine on K | UNIMOD:36 | 19 |
| Deamidated asparagine on N | UNIMOD:7 | 17 |
| N6-(2-hydroxyisobutyryl)lysine on K | UNIMOD:1849 | 16 |
| N-acetylglycine on G | UNIMOD:1 | 11 |
| N-acetylvaline on V | UNIMOD:1 | 11 |
| N6-isonicotinyllysine on K | UNIMOD:697 | 11 |
| Zinc on E | UNIMOD:954 | 11 |
| 3'-nitrotyrosine on Y | — | 10 |
| ADP-ribosylation on S | UNIMOD:213 | 10 |
| Dimethylated arginine on R | UNIMOD:36 | 9 |
| N6-crotonyllysine on K | — | 9 |
| HexNAc on Nxs | UNIMOD:43 | 8 |
| N6-benzoyllysine on K | UNIMOD:136 | 8 |
| N5-methylglutamine on Q | UNIMOD:34 | 7 |
| N6-glutaryllysine on K | — | 7 |
| Symmetric dimethylarginine on R | UNIMOD:36 | 7 |
| (3S)-3-hydroxyasparagine on N | — | 6 |
| Deamidated glutamine on Q | UNIMOD:7 | 5 |
| HexNAc on Nxt | UNIMOD:43 | 4 |
| N6-lipoyllysine on K | UNIMOD:42 | 4 |
| Tele-methylhistidine on H | UNIMOD:34 | 4 |
| Leucine methyl ester on L | UNIMOD:34 | 3 |
| N6-methacryllysine on K | — | 3 |
| S-farnesyl cysteine on C | UNIMOD:44 | 3 |
| S-glutathionyl cysteine on C | UNIMOD:55 | 3 |
| (3S)-3-hydroxylysine on K | — | 2 |
| 3-hydroxyproline on P | UNIMOD:35 | 2 |
| 5-glutamyl glycerylphosphorylethanolamine on E | UNIMOD:396 | 2 |
| 5-hydroxylysine on K | UNIMOD:35 | 2 |
| Cysteine sulfonic acid (-SO3H) on C | UNIMOD:345 | 2 |
| N-acetylcysteine on C | UNIMOD:1 | 2 |
| N-pyruvate 2-iminyl-valine on V | UNIMOD:422 | 2 |
| N6-biotinyllysine on K | UNIMOD:3 | 2 |
| N6-butyryllysine on K | UNIMOD:1289 | 2 |
| N6-malonyllysine on K | — | 2 |
| Pros-methylhistidine on H | UNIMOD:34 | 2 |
| S-(2-succinyl)cysteine on C | UNIMOD:957 | 2 |
| S-nitrosocysteine on C | UNIMOD:275 | 2 |
| 3-oxoalanine (Cys) on C | UNIMOD:402 | 1 |
| 4-hydroxylysine on K | UNIMOD:35 | 1 |
| Cysteine persulfide on C | UNIMOD:421 | 1 |
| Cysteine sulfinic acid (-SO2H) on C | UNIMOD:425 | 1 |
| Diphthamide on H | UNIMOD:375 | 1 |
| Hydroxyproline on P | UNIMOD:35 | 1 |
| Methionine sulfoxide on M | UNIMOD:35 | 1 |
| N-acetylaspartate on D | UNIMOD:1 | 1 |
| N-acetylglutamate on E | UNIMOD:1 | 1 |
| N6-1-carboxyethyl lysine on K | UNIMOD:378 | 1 |
| N6-acetyl-N6-methyllysine on K | — | 1 |
| N6-carboxylysine on K | UNIMOD:299 | 1 |
| N6-propionyllysine on K | UNIMOD:58 | 1 |
| O-palmitoyl serine on S | UNIMOD:47 | 1 |
| Phosphohistidine on H | UNIMOD:21 | 1 |
| S-cysteinyl cysteine on C | UNIMOD:312 | 1 |
| S-palmitoyl cysteine on C | UNIMOD:47 | 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
a378e8596ad8918b, written 2026-10-29T12:43:18+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