The following table contains known defects in the software, categorized by software section, with a brief abstract and information related to each defect’s severity and risk. The Item ID is the internal number assigned to each issue. Product management assesses risk, which can differ significantly from the reported severity.

Software section

Severity

Abstract

Risk

Item ID

General

High

The processing workflow fails when the study is located on the desktop (not recommended).

Low

749786

Ardia

Medium

PD server crashed after network loss.

Low

363879

CHIMERYS

Medium

The queued job was started on the CHIMERYS server, but the analysis failed due to the PC restarting automatically during Windows updates.

Low

387738

Heat map

Medium

Out-of-memory in heat map.

Low

400330

General

Medium

Protein Score is calculated wrong when using the Precursor Detector node.

Low

408138

XlinkX

Medium

Crosslinking: The localization probability is 0 for all identifications, which is not correct.

Low

416032

XlinkX

Medium

Crosslinking: XL cannot perform the analysis with the DSSO raw file acquired by an Astral instrument.

Med

418219

Ardia

Medium

There is inconsistency between the processing statistics and the job queue.

Low

424170

XlinkX

Medium

Crosslinking: XlinkX yields no results for TMT Nterm static modification.

Med

492727

Daemon

Medium

Creating the same daemon user with two separate Discoverer clients leads to a broken database.

Low

612673

Percolator

Medium

Update Percolator to the newest version on GitHub.

Low

628945

TMT

Medium

When saving a new TMT method with a correction table and there is a correction factor greater than 100% (such as, 110%), there should be a warning or stop to create this method.

Low

646306

Security

Medium

Insecure local database (not encrypted).

Low

647791

CHIMERYS

Medium

PD allows CHIMERYS results to be combined with different quan values, and the DIA Precursor table could have two columns: Area and Intensity.

Low

713421

CHIMERYS

Medium

Both CHIMERYS and CHIMERYS on Ardia failed analysis with the semi-Trypsin setting. Cloud-based CHIMERYS has detailed hint information, and CHIMERYS on Ardia should have the same hint information.

Low

754229

Export

Medium

Exported Astral .raw files to .mgf files contain no precursor mass.

Med

758266

Spectral libraries

Low

It is not possible to directly upload a large database downloaded from NCBI with the .gz format without unzipping the database.

Low

249039

MS/MS spectra

Low

The x-axis scale for the spectrum matching was larger than the fragments ion coverage area under both reference spectrum checked and unchecked.

Low

266072

Study

Low

The input files table is jumping up and down when hovering.

Low

401489

Study

Low

Importing a study from a .csv file does not work if remote files are included.

Low

403802

General

Low

.pdResult tooltip shows the wrong information.

Low

408301

CHIMERYS

Low

Validate if the settings the inclusion file was created with match the actual search to be run.

Low

409072

General

Low

Advanced Parameters button is cut off (cosmetic).

Low

409831

Mascot Communication Tester

Low

Context Help should work in the Mascot Communication tester the same as it works in the CHIMERYS Communication tester.

Low

411174

Export

Low

SpectrumTitle not used in mzML file export.

Low

420602

General

Low

Tooltips for full precision numerical values are not shown for all columns.

Low

456313

General

Low

CWF fails when the study is on a remote external SSD drive.

Low

559004

Modification editor

Low

Modification Editor does not allow the definition of modification of the same name with a different target.

Low

585101

General

Low

PCM Groups q-Value filter setting: 1E-5 shows as 0.00.

Low

593947

General

Low

Open Study and New Study options on the Start page are available even when menu pendant is disabled.

Low

595006

Job Queue

Low

Automated processing workflows appear in the wrong order in the job queue.

Low

639904

General

Low

Apply button remains disabled when layout changes.

Low

729034

FASTA

Low

RM: Errors occur when removing a FASTA file that is currently updating.

Low

743864

Display Settings node

Low

When the parameter is not valid in the node, a yellow warning exclamation sign should display.

Low

747773

General

Low

In some cases, the number of parallelized jobs seem unexpected.

Low

749783

General

Low

The hints are missing from the Execute state column in the analysis results table.

Low

752141

CHIMERYS

Low

The CHIMERYS Error Code column and the CHIMERYS Error column are missing in the table of input files for a CHY failed case.

Low

752518

XlinkX

Low

XL: The Protein Descriptions B filter is not correct on the table of Crosslinks.

Low

752543

MS Amanda

Low

MSAmanda results are not stable when repeating the same analysis.

Med

756268

General

Low

Reprocessing the CWF or creating a new CWF fails when the MSF file is opened.

Low

762767

FASTA

Low

RM: Cannot download FASTA file with and without subtaxonomies with the same TaxId.

Low

763521