Proteomics analysis of rat liver after disulfiram treatment

count_mismatch warning
The bundle holds 2.31485e+06 where the producer reported 2.3152e+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
11.33 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.

occupancy_not_stored warning
Of 460127 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 9620 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).

peptide_rows_localization_ambiguous warning
1578 row(s) of AllQuantifiedPeptides.tsv name several full sequences, joined by `|`: a peptide whose modification site the search did not settle (MetaMorpheus #2917). Their 8374 value(s) are not stored, since storing them under one of the sequences would place them on a site the search never decided. The PSMs behind them are in `psms`. E.g. `AAAEVNQ[Common Artifact:Deamidation on Q]EYGLDPK|AAAEVN[Common Artifact:Deamidation on N]QEYGLDPK`, `AADAHVDAHYYEQNEQ[Common Artifact:Deamidation on Q]PTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGN[Common Artifact:Deamidation on N]R|AADAHVDAHYYEQN[Common Artifact:Deamidation on N]EQPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGN[Common Artifact:Deamidation on N]R|AADAHVDAHYYEQN[Common Artifact:Deamidation on N]EQ[Common Artifact:Deamidation on Q]PTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR|AADAHVDAHYYEQ[Common Artifact:Deamidation on Q]NEQPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGN[Common Artifact:Deamidation on N]R|AADAHVDAHYYEQ[Common Artifact:Deamidation on Q]NEQ[Common Artifact:Deamidation on Q]PTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR|AADAHVDAHYYEQ[Common Artifact:Deamidation on Q]N[Common Artifact:Deamidation on N]EQPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR`, `AADAHVDAHYYEQNE[Metal:Fe[III] on E]QPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR|AADAHVDAHYYE[Metal:Fe[III] on E]QNEQPTGTC[Common Fixed:Carbamidomethyl on C]AAC[Common Fixed:Carbamidomethyl on C]ITGGNR`.

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: 9529 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.