The AutoPeak integration algorithm, and how it can help reduce the headache of re-integrating data by April Quinn-Paquet | Aug 7, 2021 | Algorithms, SCIEX information, SCIEX OS software, TechnologyWith higher throughput demands on today’s mass spec quantitative applications, the bottlenecks affecting sample turnaround time are moving from data acquisition to data processing. Most lab environments like this can’t afford the time it takes to re-integrate missed...
How is the protein level fold-change computed on proteomics data using Assembler app? by Christie Hunter | Aug 7, 2021 | Algorithms, Life Science Research, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemWith bottom-up proteomics, we quantify peptides in the sample and then infer the protein level quantitation from that data. However, due to post-translational modifications, different protein isoforms, etc. we don’t always expect that all peptides associated with the...
What is the Most likely ratio normalization strategy? by Christie Hunter | Aug 7, 2021 | Algorithms, Life Science Research, MarkerView, Metabolomics, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemWhen performing LC-MS quantitation, there are numerous sources of experimental variance that can confound the quality of your results (variation in the starting amount of sample, variation in the LC-MS measurements, etc.). Having a robust normalization strategy that...
What are my normalization options in MarkerView software and when should I use them? by Christie Hunter | Aug 6, 2021 | Algorithms, Data processing, MarkerView, SCIEX information, TechnologyIn 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...
What is the t-test and when should I use it? by Christie Hunter | Aug 6, 2021 | Algorithms, Data processing, MarkerView, SCIEX information, TechnologyA 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? by Christie Hunter | Aug 6, 2021 | Algorithms, Data processing, MarkerView, SCIEX information, TechnologyIn 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...
What is principal component analysis and how does it work? by Christie Hunter | Aug 6, 2021 | Algorithms, Data processing, MarkerView, SCIEX information, TechnologyWhen 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,...