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FlashLFQ protein quant columns are labelled by file name when an experimental design exists, and 'Intensity__1' when it does not

Status: Open.

#1128 In smith-chem-wisc/mzLib;

· trishorts opened on Aug 3, 2026

FlashLFQ PEP analysis writes model.zip into the input data folder, causing collisions between concurrent runs

Status: Open.

#1124 In smith-chem-wisc/mzLib;

· trishorts opened on Aug 3, 2026

Digest applies modifications after cleavage, producing peptides whose C-terminal K is modified in a way that blocks trypsin

Status: Open.

#1113 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

ProteinDbLoader silently drops glycosylation-site annotations that have a defined formula and mass (22 of 24 on albumin)

Status: Open.

#1112 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

FlashLFQ peptide roll-up nondeterministically drops MBR intensities, making protein quant irreproducible run-to-run

Status: Open.

#1111 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

ETD/ECD suppress z• ions N-terminal to proline but still emit the complementary c ions

Status: Open.

#1110 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

Protein.Digest returns duplicate peptidoforms where a chain boundary meets the initiator-Met cleavage site

Status: Open.

#1108 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

proteases.tsv: 'trypsin' and 'trypsin|P' mean the reverse of the MaxQuant/Mascot convention

Status: Open.

#1106 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

PrideArchiveClient: filename guard defeated by trailing space/dot and device names; NUL writes outside the destination

Status: Open.

#1105 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

CONTRIBUTING.md says contributions are MIT, but LICENSE is LGPL-3.0

Status: Open.

#1104 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

Referencing any part of mzLib pulls in TorchSharp/libtorch (238 MB) - measured 126 MB vs 34 MB for a PRIDE-only tool

Status: Open.

#1103 In smith-chem-wisc/mzLib;

· trishorts opened on Jul 23, 2026

Salvage variant bugfixes from closed #974/#973 (XML-writer-consensus-only, variant-list pruning, homozygous depth, mods-on-variants)

Status: Open.

#1083 In smith-chem-wisc/mzLib;

· trishorts opened on Jun 30, 2026