Parallel Channels-Multidimensional Protein Identification Technology

Multidimensional protein identification (MudPIT), developed in the Yates Laboratory 20 years ago, is regarded as a powerful tool for proteomics research. Due to its remarkable online separation advantages, MudPIT has been widely used to facilitate discoveries in the field of proteomics research. However, it has one major disadvantage: the process of eluting peptides during strong cation exchange introduces salts, of different concentrations, into the mass spectrometer. Considering the sensitivity of the new generation of high-resolution mass spectrometers, developing a new version of MudPIT that could eliminate the introduction of salts in the elute would be a significant advancement to current technology. Herein, we developed a new, clean version of MudPIT called parallel channels-multidimensional protein identification technology (PC-MudPIT) to overcome this issue. In this design, the original biphasic trapping column was replaced by two parallel analytical column channels. We successfully averted the salt contamination yet retained all the other advantages of MudPIT. A total of 8161 and 7359 protein groups were identified from A549 whole cell lysate using PC-MudPIT and classic MudPIT, respectively. Moreover, we discovered the additional advantage that, in online mode, PC-MudPIT can also be used for an enrichment process of phosphopeptide identification. We identified a total 11453 phosphopeptides using PC-MudPIT and 7729 phosphopeptides using offline TiO₂ enrichment followed by classic MudPIT. These advances indicate the possibility of other innovative applications of PC-MudPIT technology in deep proteome exploration.

Microfluidic Flow-through SPME Chip for Online Separation and MS Detection of Multiple Analyses in Complex Matrix

Simplifying tedious sample preparation procedures to improve analysis efficiency is a major challenge in contemporary analytical chemistry. Solid phase microextraction (SPME), a technology developed for rapid sample pretreatment, has flexibility in design, geometry, and calibration strategies, which makes it a useful tool in a variety of fields, especially environmental and life sciences. Therefore, it is important to study the coupling between the microfluidic electrospray ionization (ESI) chip integrated with the solid phase microextraction (SPME) module and the electrospray mass spectrometer (MS). In our previous work, we designed a solid phase microextraction (SPME) module on a microfluidic chip through geometric design. However, automation and calibration methods for the extraction process remain unresolved in the SPME on-chip domain, which will lead to faster and more accurate results. This paper discusses the necessity to design a micromixer structure that can produce different elution conditions on the microfluidic chip. By calculating the channel resistances, the microfluidic chip’s integrated module with the micromixer, SPME, and ESI emitters optimize the geometry structure. We propose the annular channel for SPME to perform the resistances balance of the entire chip. Finally, for SPME on a single chip, this work provides a quantitation calibration method to describe the distribution of the analytes between the sample and the extraction phase before reaching the adsorption equilibrium.