The following table lists defects that were resolved between Proteome Discoverer 3.1 and Proteome Discoverer 3.2. The table excludes Help issues and any cosmetic fixes. In some cases, the original abstract has been amended or expanded upon to better describe the reported issue. Both an engineering fix and follow-up testing (verified by our product evaluation department) have resolved each of these issues.

Item ID

Software section

Abstract

91748

Statistical analysis

Proteome Discoverer encounters errors in ANOVA hypothesis testing and is missing value imputation when Windows security options to use FIPS compliant algorithms for encrypting are enabled.

176735

Statistical analysis

The volcano plot not centered.

266691

XlinkX

Crosslinking: The Crosslink Sequence is empty in some cases.

357141

Fragment match view

The fragment table is not updated when the tolerance constraint is changed, or the spectrum annotation is updated.

385570

Ardia

When publishing a .pdResult file from Proteome Discover to Ardia, the .pdResult and its related files were uploaded, but not the .msf results file.

388322

XlinkX

XlinkX export to mzML fails.

395066

General

Double-clicking a .pdResult file or an .msf file does not open the file in PD.

405844

CHIMERYS

Large Datasets: CHIMERYS analysis failed with local fractions as input and the processing mode for one job for all files.

418835

General

An exception is thrown with an attempt to open a .pdResult file or .msf file outside of PD, if the application is already opened.

423952

CHIMERYS

CHIMERYS on Ardia Server crashed when running one job for all stress test with over 220+ GB of input data.

430549

XlinkX

Security: Do not use zlib.net.dll in XlinkX open search bundle.

434289

FASTA

The FASTA file cannot be completely deleted when all the FASTA files are selected for removal.

434515

Backwards compatibility

PD 3.1 could not directedly create multiconsensus results from nom-updated PD 3.0 .msf files.

441752

Sequest HT

Sequest HT reports peptides with too high a delta mass.

447867

Spectral libraries

The exported big MS Library cannot be imported into PD because of the file size limitation.

449878

XlinkX

Crosslinking: CSM ID Details view is empty for Phox XL result.

454313

XlinkX

Crosslinking: The Show Isotope Pattern of CSMs is not displayed.

459480

CHIMERYS

The CHIMERYS node allows the selection of different modifications for the same residue, which causes CHIMERYS to crash.

463295

XlinkX

There is no description for the Proforma File parameter of the XlinkX/PD Detect node in PD3.1.0.638.

468416

Export

mzML file was not exported when exporting to mzidentml.

470323

INFERYS rescoring

INFERYS failed rescoring on IT MS2 data.

523344

Ardia

When adding remote results from the Ardia server, the Object Picker should browse to the last used highlighted folder.

545598

Fragment match details

Wrong fragment identification on peptide spectrum match.

577978

Export

Text export discrepancy.

582828

Annotation

Connection issue to protein annotation service - no error information.

585413

Annotation

Execution Failed message displays for a consensus workflow when its protein annotation node fails, which is unexpected.

588004

Workflow editor

Workflow is not blocked when it is saved with a disconnected node.

602563

CHIMERYS

CHIMERYS node does not allow a search to be submitted when selecting both static and dynamic modifications.

613416

Results view

Data Distribution node does not mark samples where CHIMERYS did not find a high confident PSM but found a quan value.

634412

Annotation

Retrieval of GO graphs for annotation results in rare cases are in an endless loop.

649838

CHIMERYS

Multipart upload of CHIMERYS sometimes uploads spectra or FASTA file incorrectly.

723123

CHIMERYS

Annotated Sequence does not contain TMT modification when Peptide N-term is searched as dynamic with CHIMERYS.

741846

Daemon

Spectrum export to mzML fails in Daemon.