As a complementary strategy to in-depth analysis of biological samples, we have established methods optimized for the screening of clinical samples.
1. Rapid screening of individual serum/plasma or urine samples (intermediate to high throughput - low sensitivity)
2. Comprehensive analysis of sample groups using Expression Profiling (low throughput - higher sensitivity)
The two approaches are complementary. The first one allows analysis of individual samples in an intermediate to high throughput manner. A limitation of this approach represents the ability to detect the most abundant components only. A second approach takes advantage of the label-free expression profiling analysis. When combined with pre-fractionation, for example using the OFFGEL system (Agilent), a much larger number of components per sample can be identified. However, this approach is clearly limited in its throughput, so that samples within a group need to be pooled. The sections below describe each method in more detail.
1. Rapid screening of individual serum/plasma, urine or other body fluid samples
This method comprises a rapid mass profiling strategy based on MALDI-TOF analysis and fractionation using ClinProtTM magnetic beads (Bruker Daltonics). Different bead chemistries allow the enrichment of glycosylated, phosphorylated, antibody bound material, large proteins or peptides, providing the possibility to isolate subsets of molecules including posttranslational modifications.
This approach permits comparing a large cohort of samples and detect differences in mass profiles that can be then associated with disease progression and phenotype. The beads technology allows for scale-up and additional studies to identify new biomarkers that have been identified in screening studies. This technology is suitable for studying patient cohorts that consist of serum, plasma, urine or other body fluids. However, it should be noted that this approach is limited in detecting only the most abundant components in clinical samples.
2. Comprehensive analysis of sample groups using Expression Profiling
This method takes advantage of the label-free expression profiling technology that we have established in the lab (further described in detail under "Proteomics Techniques and Expertise"). Large-scale expression profiling data sets derived from such an analysis can be further interrogated using Ingenuity Pathway Analysis (IPA) for a systems biology type of data evaluation. This approach can provide comprehensive information about differentially regulated proteins and peptides, but can only be performed on carefully selected small sets or pooled sample groups.
In general, these complex characterizations require the setup of a collaboration prior to the initiation and during the analyses of a given project and should be discussed in detail beforehand. Such projects often require modification of our standard analytical methodologies for digestion and analysis, multiple analytical runs and extensive data mining in order to achieve the desired result. Multiple sample submissions by the researcher may be necessary in order to achieve the initial goals.