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Advancing Plasma Proteomics Analyses

Novel proteomics techniques have potential to help improve diagnosis and therapeutic decisions for patients with neurodegenerative conditions

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Blaine Roberts, PhD

Blaine Roberts, PhD, is an associate professor in the Department of Biochemistry and Department of Neurology at Emory University. He obtained his bachelor of science in chemistry at Montana State...

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Shourjo Ghose, PhD

Shourjo Ghose received his PhD in biochemistry from Montana State University and went on to do postdoctoral work at the Scripps Research Institute, followed by a business certification from Harvard...

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Neurodegenerative conditions such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis (ALS) are characterized by the progressive degeneration of the nervous system, which often leads to a range of debilitating symptoms. Early and accurate diagnosis along with effective therapeutic interventions are essential to managing such conditions. 

The challenge in diagnosing and treating neurodegenerative disease lies in their complex and multifaceted nature. Traditional diagnostic methods often rely on clinical symptoms and, in some cases, neuroimaging techniques like magnetic resonance imaging (MRI) or positron emission tomography (PET). However, these approaches do not always offer the sensitivity required to detect early-stage disease or to provide prognostic or mechanistic insight. 

Plasma proteomics 

Since as early as 1975, proteomics had become a highly regarded technique for disease research, developing biomarkers, and informing drug discovery.  It is a powerful tool to decipher the molecular basis of various diseases, including neurodegenerative conditions. From these beginnings, advances in mass spectrometry (MS) and other analytical techniques have made it possible to investigate the proteome of plasma with unprecedented precision.

Plasma proteomics offers several key insights into the diagnosis and treatment of neurodegenerative diseases. For example, by comparing the protein profiles of individuals with and without neurodegenerative conditions, researchers can identify potential biomarkers that may be associated with disease onset or progression. The discovery of such biomarkers can aid early diagnosis and help in understanding the course of the disease. Regular monitoring of plasma proteomes can also provide real-time information on disease progression and an individual’s response to therapy, enabling timely adjustments in treatment plans as needed. Identifying specific protein targets associated with neurodegenerative conditions can aid in the development of novel drugs that potentially slow or even stop disease progression.

The extra dimension

Ion mobility spectrometry (IMS) has recently been found to be a powerful complement to traditional MS analyses for the separation, identification, and quantification of peptides and proteins. The ion mobility measurements can be used to determine ion-specific collisional cross-section value (CCS), an additional dimension that allows researchers to transition from 3D proteomics (retention time, mass to charge [m/z] and MS/MS fragment ion spectra) to 4D proteomics.

Measuring CCS values is particularly useful in Alzheimer's disease research as they can help to confirm the isoform or post-translational modification being studied. Adding liquid chromatography and trapped ion mobility reveals that there are two positions on the molecule where isomerization can occur. Once there is isomerization at position seven, the amyloid beta can be resolved using the trapped ion mobility.

Trapped ion mobility spectrometry (TIMS) is a novel technique that separates ions as a function of their CCS. An electrical field controls each ion from moving beyond a certain position, which is defined by the ion’s shape in gas phase and allows the selective release of ions from the TIMS tunnel in a process called parallel accumulation-serial fragmentation (PASEF). With PASEF, the TIMS design enables the reproducible measurement of CCS values for all detected ions. These CCS values further increase the system’s selectivity, resulting in more reliable quantitation in complex samples.

Combining high MALDI sensitivity with TIMS capability 

Rapid high-resolution matrix-assisted-laser-desorption/ionization (MALDI) imaging capabilities can be added to TIMS to give researchers the unique ability to accurately correlate measured results with morphological context, resolving the spatial distribution of proteins down to 5 µm. The result is a true spatial ‘omics platform with widespread application. 

The Roberts Laboratory is a cutting-edge research lab based at the Emory University School of Medicine, in Atlanta, Georgia that uses novel proteomics techniques and advanced technologies to better understand neurodegenerative disease. Recent advancements in plasma proteomics analyses in particular have shown potential to revolutionize the diagnosis and treatment of Alzheimer's disease, Parkinson's disease, and ALS. One example from the Roberts Lab is the separation of isobaric or isomeric molecules to get the true spatial localization of the analytes–a common challenge for researchers. Combining TIMS and MALDI capabilities is currently the only method to differentiate isomers and resolve their spatial distributions. Using CCS values, the identity of an analyte can be resolved and validated with this additional quality criterion. CCS-enabled software intelligently matches spatial MALDI-TIMS imaging data with ‘omics results to add biomedically important morphological context to quantitative, isoform-resolved, proteomics data (see Figure 1).

Figure 1: Isomer separation on the timsTOF flex
Figure 1: Isomer separation on the timsTOF flex
Credit: Bruker Daltonics

With proven robust 4D-proteomics performance, the advantage of CCS measurement and the opportunity to add a spatial dimension to analysis, important molecular modifications have already been identified. The next step for The Roberts Lab is to image amyloid beta in tissue to understand whether the isomers are localized exclusively around plaques, or uniformly distributed in the grey matter of the brain. 

Toward personalized medicine approaches

Advancements in plasma proteomics analyses are opening new avenues for the early diagnosis and improved treatment of neurodegenerative conditions. By harnessing the power of molecular insights from blood-based biomarkers and the insights afforded by precise tissue imaging, a unique understanding of an individual's disease state is available. This can help predict how a patient might respond to specific therapies, which could stimulate great strides toward personalized medicine. 

As research in this field continues to evolve, we may ultimately witness a transformation in how we approach the diagnosis and treatment of neurodegenerative diseases, leading to better outcomes and an improved quality of life for those affected by these conditions.