Clinical perspectives of high‐resolution mass spectrometry–based proteomics in neuroscience—Exemplified in amyotrophic lateral sclerosis biomarker discovery research

Abstract

Biomarker discovery is a central application in today's proteomic research. There is an urgent need for valid biomarkers to improve diagnostic tools and treatment in many disorders, such as the rapidly progressing neurodegenerative disorder amyotrophic lateral sclerosis (ALS) that has a fatal outcome in about 3 years and yet no curative treatment. Screening for clinically relevant biomarkers puts high demands on high-throughput, rapid and precise proteomic techniques. There is a large variety in the methods of choice involving mainly gel-based approaches as well as chromatographic techniques for multi-dimensional protein and peptide separations followed by mass spectrometry (MS) analysis. This special feature article will discuss some important aspects of MS-based clinical proteomics and biomarker discovery in the field of neurodegenerative diseases and ALS research respectively, with the aim to provide a prospective view on current and future research aspects in the field. Furthermore, examples for application of high-resolution MS-based proteomic strategies for ALS biomarker discovery will be demonstrated with two studies previously reported by our group. These studies include among others, utilization of capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) for advanced protein pattern classification in cerebrospinal fluid (CSF) samples of ALS patients as well as highly sensitive protein identification in minimal amounts of postmortem spinal cord tissue and laser micro-dissected motor neurons using FT-ICR-MS in conjunction with nanoflow LC coupled to matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (LC-MALDI-TOF-TOF-MS).

Review: Identifying patient subtypes in multiple sclerosis and tailoring immunotherapy: challenges for the future

“…Similarly, the study of proteins, lipids and other metabolites will provide different types of information that rapidly reflect ongoing physiological processes. However, robust platforms to effectively pursue the latter classes of biomarker discovery projects are only now beginning to emerge [Ekegren et al 2008;Steinman, 2008], and we will therefore focus our discussion on RNA for which quantitative methods are relatively robust, are widespread and have well-known limitations. Published efforts in this field have recently been well summarized elsewhere [Miller et al 2008], and while much has been done in this arena, particularly with IFNb response, we have yet to deploy or even assess a clinical test.…”

Neuroproteomics tools in clinical practice

“…In our laboratory we have been studying the neuroproteome since early 2000 developing and applying novel sample preparation and proteomic approaches in neurodegenerative diseases [7][8][9][10][11][12][13][14][15][16][17]. There are many other tools available for proteomic research including protein microarrays [18], proximity ligation assay [19], Luminex-based multiplex assay [20,21], Bio-Plex assay [22], etc.…”

Clinical and laboratory features of ALS

“…SWATH has its own benefits compared with other MS labelling technology SILAC and iTRAQ. First of all it is a label-free MS technology, avoids the large variation of labeling efficiency in iTRAQ [263] . The prerequisite of MS labelling is that the targeted proteins have been screened out.…”

“…For example, neurofilaments are released from damaged axons, and are a promising biomarker in ALS [262] . There are also studies using proteomics, which uses a hypothesis free approach that is well suited for discovery of new biomarkers [263] . Blood and CSF are the biofluids most often used to search for biomarkers [264] .…”

“…It is a label free technology that offers an approach to quantify all the analytes in a sample [131] . Thus SWATH enables comprehensive protein quantitation in relatively complex samples such as plasma or serum [263] .…”