Contact closure can be used to control external devices that are not directly controlled by SCIEX OS software. A sample batch is first created in the SCIEX OS software for MS acquisition, and then a similar batch is created on an external LC device with the required...
Author Highlights
Christie Hunter
Christie Hunter is the Director of Applications at SCIEX. Christie has worked at SCIEX for 20 years, pioneering many workflows in quantitative proteomics. Christie was an early user of SWATH acquisition and played a big role in evolving the workflows and driving adoption of this new data independent approach with many proteomic researchers. Christie and her team are focused on developing and testing innovative MS workflows to analyze biomolecules, and work collaboratively with the instrument, chemistry and software research groups.
Controlling the NanoLC 425 HPLC system using contact closure in SCIEX OS software
SCIEX OS software can support external devices that are not under direct control by using contact closure. Contact closure enables synchronization of the SCIEX OS software controlled device (the MS) and the external device (the LC in this case), ensuring that...
Guidance for source tuning on the OptiFlow Pro ion source
The OptiFlow Pro ion source is the fourth generation of source in the Turbo V ion source family. Fundamental to this family of sources is the orthogonal spray design with V heater configuration, which focuses heat in the optimal spot to achieve high sensitivity...
Using Scheduled MRM algorithm in SCIEX OS software
When very large numbers of MRM transitions are monitored in a single acquisition method, the time spent acquiring data on a single analyte drops significantly. Thus, it is typical to schedule the acquisition of MRM transitions only around their time of elution, such...
What are my normalization options in MarkerView software and when should I use them?
In an LC-MS experiment there are multiple sources of variance that can confound the quality of your results. This variation can be biological e.g. differences between treated and control groups, but can also be non-biological, usually from small variations in...
How does metadata persist from the Analyst software batch into MarkerView software?
Did you know that MarkerView software can pull information directly from the metadata of your sample datafiles that can help with downstream data processing? To facilitate this, when building your batch in Analyst software, make sure to define your experimental groups...
What is the t-test and when should I use it?
A t-test (sometimes called Student’s t-test) is used to determine if the means of two sample groups are significantly different. So, for LC-MS data, we would typically use a t-test to find out if the amount of our variable of interest (protein, peptide, small...
What is principal component variable grouping (PCVG) and how do I use it?
In our previous post we discussed how to interpret the Scores and Loadings Plots produced by PCA. In many cases there are several dimensions that are found to have substantial influence over a specific principal component, and these dimensions are often correlated in...
How do I interpret the output from PCA?
Principal component analysis (PCA) is a data transformation technique that can be used to reduce the complexity of high-dimensional data sets (such as mass spectrometry data) while grouping samples based on common features. REMINDER! Principal components are linear...
What is principal component analysis and how does it work?
When we measure anything, the resulting measurements are often referred to as variables or dimensions. For example, a cube has three dimensions that can be measured: length, width and height. When we measure a complex sample using mass spectrometry (like a proteome,...
Peptide grouping in ProteinPilot software 5.0
A new feature in ProteinPilot software 5.0 is the ability to do peptide grouping. When analyzing proteomics data from LC-MS/MS, one must take into account the multiple pieces of evidence supporting a peptide as well as any ambiguity that might still exist in the...
Quickly compare identification results from ProteinPilot software
When a ProteinPilot Software search is complete, a ProteinPilot report is generated that contains all the false discovery rate (FDR) analysis information. More information on using the large and small ProteinPilot reports can be found here When doing method...