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What is the difference between MRM3 vs MS/MS/MS (MS3)?
The MRM3 workflow and the MS3 scan are functionally the same QTRAP system scan, but used with different goals in mind. The main difference is how these scans are used in the whole MS workflow. With MS3 scans, you can use these in a data dependent mode for discovery where you can trigger MS/MS/MS scans […]
Tags: analyst, article, book, computer, data, experiment, file, form, fragment, guide, information, item, knowledge, loop, machine, perform, research, scan, script, software
August 8, 2021
Protocol for offline trap washing with NanoLC 425 system
Using the dual gradient system, the nanoLC 425 system can be configured such that the trap can be washed to waste rather than through the column and into the mass spectrometer. This workflow can be performed with either nanoflow or microflow chromatography. Figure 1. Example of washing the late-eluting compounds to waste. In a typical […]
August 7, 2021
Analysis of chiral amphetamines using differential mobility separation (DMS)
Many compounds are challenging to analyze because they are isomers (have the same m/z) and also sometimes have the same HPLC retention time. And to make it even more complicated, sometimes there are two chiral forms that have different functions in biology, making it very critical to be able to differentiate them and quantify them […]
Separating cyclosporin isomers using differential mobility separation (DMS)
Cyclosporin A (CsA) has been a very successful immunosuppressant for preventing organ transplant rejection. It is a large cyclic peptide (11 residues, ~1200 Da) and there are numerous modifications of this drug, some of which are isomers. The challenge of analyzing isomers by mass spectrometry is obvious, if they have the same mass and retention […]
Using Bio Tool Kit for interpreting peptide MS/MS data obtained using electron activated dissociation (EAD)
Peptide MS/MS spectra obtained using either collision induced dissociation (CID) or electron activated dissociation (EAD) can be analyzed using the Peptide Fragments pane in Bio Tool Kit in SCIEX OS Software. First, open the EAD MS/MS spectrum that you want to interpret. Then, launch the Peptide Fragments pane from the Bio Tool Kit menu. To […]
- Bio Tool Kit
- Biopharma
- Data processing
- Data Visualization
- Life Science Research
- Proteomics
- QTOF
- SCIEX information
- Technology
- ZenoTOF 7600 system
Tags: EAD, fragmentation
Peptide fragmentation using electron activated dissociation (EAD)
Most workflows in protein quantification and characterization by mass spectrometry have used collision-induced dissociation (CID). In the CID process, a peptide is selected in the first quadrupole of the instrument (Q1), then accelerated through a collision cell where it collides with nitrogen gas. The collision energy, at which the peptide is moved through this region […]
- Bio Tool Kit
- Biopharma
- Data acquisition
- Life Science Research
- Proteomics
- SCIEX information
- Technology
- ZenoTOF 7600 system
Tags: EAD, fragmentation, peptide
Automatic calibration in minutes for microflow LC with the OptiFlow source on ZenoTOF 7600 system
The OptiFlow ion source for the SCIEX ZenoTOF 7600 system is equipped with an ESI calibration probe for automatic calibration during microflow experiments (diagram below). The ESI probe is installed orthogonal to the microflow probe in the OptiFlow source and connected to the integrated calibrant delivery system (CDS). Calibrant solutions are infused from the CDS […]
What is the Zeno threshold and what does it do?
With the introduction of the Zeno trap on the ZenoTOF 7600 system, sensitivity improvements on the order of 4 to 25x can be seen for MS/MS analysis, because of the optimization of duty cycle.1 When concentrations are low and peak intensities are limited, this bump in sensitivity is definitely desirable. But what about when peak […]
- Bioanalysis/PK
- Data acquisition
- Lipidomics
- Metabolomics
- Multi-Omics
- Proteomics
- SCIEX information
- SCIEX OS software
- Technology
- Toxicology
- ZenoTOF 7600 system
Tags: acquisition, precursor, threshold, trap, Zeno
Tips and tricks: setting up LC-MS/MS methods for lipid mediator profiling
Starting up a workflow for lipid mediator analysis can be challenging. Hundreds of distinct fatty acid-derived molecules can be produced biologically (i.e., enzymatically) and/or via non-enzymatic routes. Additionally, various biosynthetic pathways yield both bioactive mediators as well as side-products, intermediates, and metabolites that may not always be of interest for labs focused on select biomarkers, […]
Importing processing methods from Analyst or MultiQuant software to SCIEX OS-MQ software
SCIEX OS-MQ software is the latest innovation from SCIEX in fast, reliable data processing and streamlined review. Combining the powerful features of multiple software platforms into one, it’s a single solution for your data processing needs. But you don’t have to start from scratch! Full MultiQuant software processing methods can be imported from components to […]
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