ナレッジベース資料（FAQ）

ProteinPilot™ software 5.0.3 is needed to view group files from OneOmics™ suite

In order to view group files generated by ProteinPilot™ software from the OneOmics™ suite, users must install ProteinPilot software 5.0.3, a beta version of the software that is not currently available from the SCIEX software downloads page. The link to the installer is provided in this article.

Why Can't Users with Non-US English Language Settings Create an FDR Report in ProteinPilot™ Software?

When running a search in ProteinPilot™ software as an admin or non-admin user, there should be no difference in FDR report creation as long as full Windows permissions have been provided for Excel report creation. For ProteinPilot software version 5.0.2 with the latest patch (ProteinPilot 5.0.2 Patch for UniProt Issue - Rev. 2), users with a non-admin role may not be able to create reports if the language and font settings are not set to US English.

Where Are the Log Files Located for ProteinPilot™ Software?

The log files are needed for troubleshooting error messages in ProteinPilot™ software and can be located at C:\AB SCIEX\ProteinPilot Data\Temp\ProteinPilot.log.

Decreasing Run Time when Using the LCMS Reconstruct Algorithm in ProteinPilot™ Software｜質量分析計・LC-MS/MSシステムのSCIEX

This article describes how to modify the configuration file for ProteinPilot™ software to decrease the time needed when using the LSMS Reconstruct algorithm, especially when performing large protein ID searches on data sets from a TripleTOF® 6600 LC-MS/MS System.

Can ProteinPilot™ Software Version 5.0.2 Be Installed on a 2019 Server?｜質量分析計・LC-MS/MSシステムのSCIEX

Yes, ProteinPilot™ software 5.0.2 can be run on a Windows 2019 Server. This was not officially tested or mentioned in the release notes, but many users have installed the Windows 10-compatible ProteinPilot software 5.0.2 on the Windows Server 2019 operating system and have run the software successfully in this environment.

Can Wiff1 Files Generated by SCIEX OS Software 2.1 from X500 Series Instruments be Searched with ProteinPilot™ Software?｜質量分析計・LC-MS/MSシステムのSCIEX

X500 series instruments generate wiff2 file formats, but with the newest version of SCIEX OS Software 2.1, they can also generate a .wiff1 file. Only .wiff1 files can be used to perform a ProteinPilot™ software search.

Can I Submit mzIdentML Files from ProteinPilot™ Software 5.x to the PRIDE Repository?｜質量分析計・LC-MS/MSシステムのSCIEX

This article summarizes the issues with ProteinPilot version 5.0 and mzIdentML created files. Submission of mzIdentML files is still not automated with later versions of ProteinPilot™ software, including version 5.0.x. Complete submissions from ProteinPilot software to PRIDE are not possible, but partial submissions of the mzIdentML are, and this partial submission process is described below.

Unable to Open SCIEX Cloud ProteinPilot™ Software Searches with the Desktop Version 5.0.2｜質量分析計・LC-MS/MSシステムのSCIEX

The version of ProteinPilot™ Software in the SCIEX Cloud is version 5.0.3; therefore, group files created in the SCIEX Cloud cannot be downloaded to a desktop and opened in ProteinPilot Software 5.0.2. To download and read a group file on a desktop installation of ProteinPilot Software, the desktop version must be upgraded to version 5.0.3.

ProteinPilot™ Search Error: Unhandled Exception: Out Of Memory Exception｜質量分析計・LC-MS/MSシステムのSCIEX

During a search with ProteinPilot™ Software 5.0, 5.0.1 and 5.0.3, the error "Unhandled Exception: Out Of Memory Exception" appears. This issue is due to the LC/MS reconstruct crashing within the ProteinPilot Software when data sets with a high MS1 scan speed are being processed.

Creating a ProteinPilot Software Winner Proteins Results List as FASTA File｜質量分析計・LC-MS/MSシステムのSCIEX

This article describes the steps for creating a FASTA file from a ProteinPilot™ software report of winner proteins.

Installing ProteinPilot™ 4.5 and 5.0.x Software on the Same PC｜質量分析計・LC-MS/MSシステムのSCIEX

For software users who need to view the older group files, maintaining a separate computer with ProteinPilot™ software 4.0 installed is the recommended best approach. Alternatively, both versions, 5.0.x and an older version, can be installed on the same computer, but this is an unsupported configuration.

Accessing ProteinPilot™ Software Searching in the SCIEX Cloud Workspace｜質量分析計・LC-MS/MSシステムのSCIEX

To log into the SCIEX Cloud workspace and access the ProteinPilot™ software searching features with just your CloudConnect license, follow the instructions below.

Missing Columns when Exporting the Protein Summary from ProteinPilot™ Software 5.0.2?｜質量分析計・LC-MS/MSシステムのSCIEX

This is a known issue in the ProteinPilot™ software 5.0.2 and was resolved with a patch.

Causes of the taglet.exe Error in ProteinPilot™ Software｜質量分析計・LC-MS/MSシステムのSCIEX

The taglet.exe error in ProteinPilot™ software is due to a wide range of issues including incorrect language settings, installation of the software on the incorrect operating system, and the incorrect addition of modifications — to name a few.

Does ProteinPilot™ Software 5.0.2 Support MALDI TOF/TOF™ Systems?｜質量分析計・LC-MS/MSシステムのSCIEX

Description of which ProteinPilot™ software versions still support 4800 and 5800 MALDI TOF/TOF™ systems.

Are CloudConnect and SWATH® MicroApps within PeakView® Software Windows 10 Compatible?｜質量分析計・LC-MS/MSシステムのSCIEX

The software package, PeakView® 2.2, CloudConnect 1.2 beta and SWATH® 2.0.1 software. is needed to perform the OneOmics workflow and/or SWATH protein data processing and is Windows 7 and Windows 10, 64-bit compatible.

Searching an EST or Other Nucleotide Databases in ProteinPilot™ Software｜質量分析計・LC-MS/MSシステムのSCIEX

Searching an EST or other types of nucleotide databases in ProteinPilot™ software requires that the database be translated first.

How Do You Export a Library in LibraryView™ 1.0.1 Software?｜質量分析計・LC-MS/MSシステムのSCIEX

The export of a library from LibraryView™ 1.0.1 software is described here.

Difference between Rapid and Thorough Searches in ProteinPilot™ Software｜質量分析計・LC-MS/MSシステムのSCIEX

The rapid search and a thorough search settings in ProteinPilot™ software determine which parts of the search algorithm will be invoked and effectively how deep the sample will be searched to find the right answers.

Will ProteinPilot™ 5.0.2 Software Function on a Windows 7 64-Bit System?｜質量分析計・LC-MS/MSシステムのSCIEX

ProteinPilot™ 5.0.2 software has only been tested on Windows 10 SP1 64-bit with Microsoft Office version 2016.

Compatibility of ProteinPilot Software 4.5 Beta with Microsoft Office 2016｜質量分析計・LC-MS/MSシステムのSCIEX

ProteinPilot software 4.5 beta is not compatible with Microsoft Office 2016.

Creating a Peptide Library in Skyline with a ProteinPilot™ 5.0 Software .Group File｜質量分析計・LC-MS/MSシステムのSCIEX

If a user installs ProteinPilot™ 5.0 software with Skyline, old and new group files will not be able to be opened because the converter has changed. An error message will be displayed when building peptide libraries while importing a ProteinPilot group file.

ProteinPilot™ 5.x Software: Incorrect Result Output for Instrument Names in the Group File｜質量分析計・LC-MS/MSシステムのSCIEX

ProteinPilot™ software uses the incorrect mass spectrometer name in its group file output file. When a TripleTOF® 5600 system was selected, the group file contains the name QSTAR® Elite instead for system information. This causes the wrong results to be output; if the incorrect instrument name is used, then the incorrect tolerance settings are applied.

ProteinPilot Software Datafile Cannot be Searched because two files are acquired under same file name｜質量分析計・LC-MS/MSシステムのSCIEX

Searching for ProteinPilot software files using Windows Explorer cannot be done because there are two files acquired under the same file name. This is a long known issue for all ProteinPilot versions that only one file per file name can be searched using ProteinPilot software.

What Default URL Is Used for Configuring the Mascot Server with ProteinPilot™ Software?｜質量分析計・LC-MS/MSシステムのSCIEX

Configuring the Mascot server from the ProteinPilot™ software requires the default URL to be used.

What is the IP Address Used by the Uniprot Server to Submit a ProteinPilot™ Software 5.x Search?｜質量分析計・LC-MS/MSシステムのSCIEX

This article describes the website links that are being used to submit a ProteinPilot™ software (v 5.x) search.

ProteinPilot™ Software 5.0: What Are the Criteria for Including a Peptide in the Feature Tab?｜質量分析計・LC-MS/MSシステムのSCIEX

The general filters for peptides are listed here. These are applied through the feature tab in ProteinPilot™ software.

What Is a Fraglet.exe Error when Running ProteinPilot™ Software 5.0?｜質量分析計・LC-MS/MSシステムのSCIEX

A "Fraglet-exe-Error" can have many causes within the ProteinPilot™ software. In some cases, this error is caused when installing ProteinPilot on an incompatible operating system.

Considerations for Bin Sizes when Creating a TOF Acquisition Method in Analyst® TF Software｜質量分析計・LC-MS/MSシステムのSCIEX

What does "bin size" mean and what is the rule of thumb for setting bin sizes when setting up acquisition methods for a TOF MS system in Analyst® TF software.

Why doesn't a TrEMBL FASTA file work for a ProteinPilot search?｜質量分析計・LC-MS/MSシステムのSCIEX

This is a known issue, and the TrEMBL database is not recommended for use with ProteinPilot software. The TrEMBL database is automatically annotated and not reviewed and could contain redundancies in terms of protein sequences, protein ascension numbers, etc.

How many processing cores will my ProteinPilot Software use?｜質量分析計・LC-MS/MSシステムのSCIEX

The number of processing cores used by ProteinPilot Software is defined by the license file and the physical capabilities of the instrument.

ProteinPilot error fraglet.exe CHEMICAL EXCEPTION｜質量分析計・LC-MS/MSシステムのSCIEX

ProteinPilot error fraglet.exe CHEMICAL EXCEPTION

How do I search an EST or other nucleotide database｜質量分析計・LC-MS/MSシステムのSCIEX

How do I search an EST or other nucleotide database

Why are the peaks centroided in ProteinPilot Group files｜質量分析計・LC-MS/MSシステムのSCIEX

Why are the peaks centroided in ProteinPilot Group files

How do I reset values or changes made in the ParameterTranslation file or ProteinPilotDataDictionary file in ProteinPilot｜質量分析計・LC-MS/MSシステムのSCIEX

It may be required to reset the values within these files if they have been manually adjusted incorrectly.

Can I use the Proteinpilot SW with 4700 data｜質量分析計・LC-MS/MSシステムのSCIEX

Can I use the Proteinpilot SW with 4700 data

fraglet.exe not wellformed invalid token at line 1 and position 33112not wellformed invalid token at line 3 and position 71｜質量分析計・LC-MS/MSシステムのSCIEX

ProteinPilot gives the error fraglet.exe not wellformed invalid token at line 1 and position 33112not wellformed invalid token at line 3 and position 71

Can I reverse the flow on my Eksigent Nano Chrom XP C18 column when experiencing high back pressure｜質量分析計・LC-MS/MSシステムのSCIEX

Can I reverse the flow on my Eksigent Nano Chrom XP C18 column when experiencing high back pressure

How to install ProteinPilot 4.5b and upgrade from ProteinPilot 4.0 to ProteinPilot 4.5b｜質量分析計・LC-MS/MSシステムのSCIEX

This procedure describes the removal and install of ProteinPilotTM software 4.5b in great detail.