Automated serum peptide profiling

Reproducibility of serum protein profiling by systematic assessment using solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Protein profiling of human serum by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) is potentially a new diagnostic tool for early detection of human diseases, including cancer. Sample preparation is a key issue in MALDI MS and the analysis of complex samples such as serum requires optimized, reproducible methods for handling and deposition of protein samples. Data acquisition in MALDI MS is also a critical issue, since heterogeneity of sample deposits leads to attenuation of ion signals in MALDI MS. In order to improve the robustness and reproducibility of MALDI MS for serum protein profiling we investigated a range of sample preparation techniques and developed a statistical method based on repeated analyses for evaluation of protein-profiling performance of MALDI MS. Two different solid-phase extraction (SPE) methods were investigated, namely custom-made microcolumns and commercially available magnetic beads. Using these two methods, nineteen different sample preparation methods for serum profiling by MALDI MS were systematically tested with regard to matrix selection, stationary phase, selectivity, and reproducibility. Microcolumns were tested with regard to chromatographic properties; reversed phase (C8, C18, SDB-XC), ion-exchange (anion, weak cation, mixed-phase (SDB-RPS)) and magnetic beads were tested with regard to chromatographic properties; reversed phase (C8) or affinity chromatography (Cu-IMAC). The reproducibility of each sample preparation method was determined by enumeration and analysis of protein signals that were detected in at least six out of nine spectra obtained by three triplicate analyses of one serum sample.A candidate for best overall performance as evaluated by the number of peaks generated and the reproducibility of mass spectra was found among the tested methods. Up to 418 reproducible peaks were detected in one cancer serum sample. These protein peaks can be part of a possible diagnostic profile, suggesting that this sample preparation method and data acquisition approach is suitable for large-scale analysis of serum samples for protein profiling.

Serum Peptide Profiling using MALDI Mass Spectrometry

Blood represents a convenient diagnostic specimen for clinical analysis. Serum metabolites and peptides have the potential to serve as reliable indicators of progression from a normal to a diseased state. However, the presence of salts, lipids and high concentrations of protein in blood serum can adversely affect its mass spectrometric profiling, as all of these moieties can hinder the ionisation and detection of diagnostic biomarkers. Several pre-fractionation strategies using chromatographic adsorbents have been employed to desalt samples and remove abundant proteins such as albumin and immunoglobulin. As an alternative to multi-stage fractionation chromatography, we describe in this practical review the adaptation and validation of a simple and fast solid-phase extraction technique using ZipTips. The protocol allows for the purification and concentration of peptides in a few, mostly automated steps, prior to spectral biomarker pattern diagnostics using MALDI MS and MS/MS. It has the added advantages of being suitable for use in a high-throughput and potentially clinical environment, only requiring a few microlitres of serum. We have evaluated, optimised, and standardised a number of analytical parameters ranging from serum storage and handling to automated peptide extraction, crystallisation, spectral acquisition, and signal processing. Using standardised protocols the average CV of serum profiles within- and between-run replicates has been evaluated and found to be around 10 % based on the variability of all detected peaks (more than 100 peaks per profile). The results show that this easy and fast method of using ZipTips, tested over a whole year, is more reproducible and more suitable for serum profile screening than magnetic bead-based methodologies which show higher variability and higher rates of rejected, low-quality spectra upon applying strict data quality control filters.

Data analysis of assorted serum peptidome profiles

Discovery of biomarker patterns using proteomic techniques requires examination of large numbers of patient and control samples, followed by data mining of the molecular read-outs (e.g., mass spectra). Adequate signal processing and statistical analysis are critical for successful extraction of markers from these data sets. The protocol, specifically designed for use in conjunction with MALDI-TOF-MS-based serum peptide profiling, is a data analysis pipeline, starting with transfer of raw spectra that are interpreted using signal processing algorithms to define suitable features (i.e., peptides). We describe an algorithm for minimal entropy-based peak alignment across samples. Peak lists obtained in this way, and containing all samples, all peptide features and their normalized MS-ion intensities, can be evaluated, and results validated, using common statistical methods. We recommend visual inspection of the spectra to confirm all results, and have written freely available software for viewing and color-coding of spectral overlays.

Opportunities and limitations of SELDI-TOF-MS in biomedical research: practical advices

Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, or surface-enhanced laser desorption/ionization ProteinChip technology, has been widely used in obtaining the quantitative profiles of tissue proteomes, particularly plasma proteomes. Its high-throughput nature and simplicity in its experimental procedures have allowed this technology to become a popular research tool for biomarker discovery in the past 5 years. After accumulating more research experiences, researchers now have a better understanding of the characteristics and limitations of this technology, as well as the pitfalls in biomarker research, by undertaking a comparative proteomic approach. This review provides an overview of the surface-enhanced laser desorption/ionization time-of-flight mass spectrometry, discusses its limitations and provides some possible solutions to help apply this technology to biomarker research.