知识库文章

Setting up a single-injection CID/EAD data-dependent acquisition (DDA) method for the ZenoTOF 7600 system

In SCIEX OS software versions 3.0 and greater, two information-dependent acquisition (IDA) methods can be created in the same acquisition method: one for electron-activated dissociation (EAD) and one for collision-induced dissociation (CID) fragmentation.

How to fix a blocked capillary on the PA 800 Plus system

Crystallized reagents on the capillary tip can cause a blocked capillary on the PA 800 Plus system, resulting in no peaks or low signal. This article explains how to clean the cartridge, capillary tips, and cartridge seal and how to perform a manual pressure rinse if the cartridge is blocked.

Middle-down sMRM HR acquisiton method setup using EAD fragmentation on the ZenoTOF® 7600 system

This article describes the parameters for evaluating subunit proteins using electron-activated dissociation (EAD) fragmentation on the ZenoTOF® 7600 system. Specific values for a successful middle-down, high-resolution sMRM acquisition method using EAD fragmentation are provided. Choosing a low, medium, and high charge state of the protein envelope is critical to get the most diverse fragmentation.

Bio Tool Kit microapp cannot manually sequence peptide MS/MS data from EAD-derived fragments

The Bio Tool Kit microapp embedded in PeakView® or SCIEX OS software cannot perform de novo manual sequencing or MS/MS fragment matching for peptides fragmented using electron activated dissociation (EAD) on a ZenoTOF 7600 system. The MS/MS data obtained by EAD is too complex and fragment-rich, presenting the software with too many options for potential fragment ions; however, the Bio Tool Kit app can process MS/MS data acquired by CID (collision-induced dissociation).

How to use Bio Tool Kit for interpreting peptide MS/MS data acquired with CID and EAD fragmentation?

The Bio Tool Kit and its Peptide Fragments feature is tremendously helpful when trying to interpret MS/MS peptide data. This can be adjusted to either CID (collision-induced dissociation) or EAD (electron activated dissociation). A glycopeptide example for EAD and CID is described.

Processing oligonucleotides using Bio Tool Kit software

The Bio Tool Kit software can deconvolute oligonucleotides in negative mode using the Reconstruct Protein option. The Bio Tool Kit microApp is embedded in the PeakView™ or SCIEX OS software and requires an additional license to activate these features.

Adding a new ADC linker to Biologics Explorer software

There are two options for adding an antibody-drug conjugate (ADC) linker in Biologics Explorer software for use in intact protein and peptide mapping workflows: 1) as a custom modification using the Modification Editor or 2) as direct additions into the Conjugates tab in the Protein Mapping - Settings window.

Adding workflow templates to Biologics Explorer software without the template manager

Biological Explorer software uses workflow templates that are typically packaged into the software using a built-in template manager. If the template manager is not working, then templates can be added to the Biologics Explorer software by transferring them to a specific file path on the C drive: C:\ProgramData\SCIEX\BiologicsExplorer\templates.

Locating the Name of a Server or PC Using the Command Prompt Window

This article describes the DOS commands used to access the name of the server or PC.