According to Genome Sequencing Project statistics (http://www.ncbi.nlm.nih.gov/genomes/static/gpstat.html), as of Feb 16, 2012, complete gene sequences have become available for 2816 viruses, 1117 prokaryotes, and 36 eukaryotes.1–2 The availability of full genome sequences has greatly facilitated biological research in many fields, and has greatly contributed to the growth of proteomics.

Proteins are important because they are the direct bio-functional molecules in the living organisms. The term “proteomics” was coined from merging “protein” and “genomics” in the 1990s.3–4 As a post-genomic discipline, proteomics encompasses efforts to identify and quantify all the proteins of a proteome, including expression, cellular localization, interactions, post-translational modifications (PTMs), and turnover as a function of time, space and cell type, thus making the full investigation of a proteome more challenging than sequencing a genome. There are possibly 100,000 protein forms encoded by the approximate 20,235 genes of the human genome,5 and determining the explicit function of each form will be a challenge.

The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis. Mass spectrometry has emerged as a core tool for large-scale protein analysis. In the past decade, there has been a rapid advance in the resolution, mass accuracy, sensitivity and scan rate of mass spectrometers used to analyze proteins. In addition, hybrid mass analyzers have been introduced recently (e.g. Linear Ion Trap-Orbitrap series6–7) which have significantly improved proteomic analysis.

“Bottom-up” protein analysis refers to the characterization of proteins by analysis of peptides released from the protein through proteolysis. When bottom-up is performed on a mixture of proteins it is called shotgun proteomics,8–10 a name coined by the Yates lab because of its analogy to shotgun genomic sequencing.11 Shotgun proteomics provides an indirect measurement of proteins through peptides derived from proteolytic digestion of intact proteins. In a typical shotgun proteomics experiment, the peptide mixture is fractionated and subjected to LC-MS/MS analysis. Peptide identification is achieved by comparing the tandem mass spectra derived from peptide fragmentation with theoretical tandem mass spectra generated from in silico digestion of a protein database. Protein inference is accomplished by assigning peptide sequences to proteins. Because peptides can be either uniquely assigned to a single protein or shared by more than one protein, the identified proteins may be further scored and grouped based on their peptides. In contrast, another strategy, termed ‘top-down’ proteomics, is used to characterize intact proteins (Figure 1). The top-down approach has some potential advantages for PTM and protein isoform determination and has achieved notable success. Intact proteins have been measured up to 200 kDa,12 and a large scale study has identified more than 1,000 proteins by multi-dimensional separations from complex samples.13 However, the top-down method has significant limitations compared with shotgun proteomics due to difficulties with protein fractionation, protein ionization and fragmentation in the gas phase. By relying on the analysis of peptides, which are more easily fractionated, ionized and fragmented, shotgun proteomics can be more universally adopted for protein analysis. In fact, a hybrid of bottom-up and top-down methodologies and instrumentation has been introduced as middle-down proteomics.14 Essentially, middle-down proteomics analyzes larger peptide fragments than bottom-up proteomics, minimizing peptide redundancy between proteins. Additionally the large peptide fragments yield similar advantages as top-down proteomics, such as gaining further insight into post-translational modifications, without the analytical challenges of analyzing intact proteins. Shotgun proteomics has become a workhorse for the analysis of proteins and their modifications and will be increasingly combined with top-down methods in the future.



Figure 1

Proteomic strategies: bottom-up vs. top-down vs. middle-down. The bottom-up approach analyzes proteolytic peptides. The top-down method measures the intact proteins. The middle-down strategy analyzes larger peptides resulted from limited digestion or ...



In the past decade shotgun proteomics has been widely used by biologists for many different research experiments, advancing biological discoveries. Some applications include, but are not limited to, proteome profiling, protein quantification, protein modification, and protein-protein interaction. There have been several reviews nicely summarizing mass spectrometry history,15 protein quantification with mass spectrometry,16 its biological applications,5,17–26 and many recent advances in methodology.27–32 In this review, we try to provide a full and updated survey of shotgun proteomics, including the fundamental techniques and applications that laid the foundation along with those developed and greatly improved in the past several years.

Protein Analysis by Shotgun/Bottom-up Proteomics

Capillarity and Wetting Phenomena: Drops, Bubbles, Pearls, Waves

Precise and effective control of droplet generation is critical for applications of droplet microfluidics ranging from materials synthesis to lab-on-a-chip systems. Methods for droplet generation can be either passive or active, where the former generates droplets without external actuation, and the latter makes use of additional energy input in promoting interfacial instabilities for droplet generation. A unified physical understanding of both passive and active droplet generation is beneficial for effectively developing new techniques meeting various demands arising from applications. Our review of passive approaches focuses on the characteristics and mechanisms of breakup modes of droplet generation occurring in microfluidic cross-flow, co-flow, flow-focusing, and step emulsification configurations. The review of active approaches covers the state-of-the-art techniques employing either external forces from electrical, magnetic and centrifugal fields or methods of modifying intrinsic properties of flows or fluids such as velocity, viscosity, interfacial tension, channel wettability, and fluid density, with a focus on their implementations and actuation mechanisms. Also included in this review is the contrast among different approaches of either passive or active nature.

Passive and active droplet generation with microfluidics: a review

Fogging occurs when moisture condensation takes the form of accumulated droplets with diameters larger than 190 nm or half of the shortest wavelength (380 nm) of visible light. This problem may be effectively addressed by changing the affinity of a material’s surface for water, which can be accomplished via two approaches: i) the superhydrophilic approach, with a water contact angle (CA) less than 5°, and ii) the superhydrophobic approach, with a water CA greater than 150°, and extremely low CA hysteresis. To date, all techniques reported belong to the former category, as they are intended for applications in optical transparent coatings. A well-known example is the use of photocatalytic TiO2 nanoparticle coatings that become superhydrophilic under UV irradiation. Very recently, a capillary effect was skillfully adopted to achieve superhydrophilic properties by constructing 3D nanoporous structures from layer-by-layer assembled nanoparticles. The key to these two “wet”-style antifogging strategies is for micrometer-sized fog drops to rapidly spread into a uniform thin film, which can prevent light scattering and reflection from nucleated droplets. Optical transparency is not an intrinsic property of antifogging coatings even though recently developed antifogging coatings are almost transparent, and the transparency could be achieved by further tuning the nanoparticle size and film thickness. To our knowledge, the antifogging coatings may also be applied to many fields that do not require optical transparency, including, for example, paints for inhibiting swelling and peeling issues and metal surfaces for preventing corrosion. These types of issues, which are caused by adsorption of moisture, are hard to solve by the superhydrophilic approach because of its inherently “wet” nature. Thus, a “dry”-style antifogging strategy, which consists of a novel superhydrophobic technique that can prevent moisture or microscale fog drops from nucleating on a surface, is desired. Recent bionic researches have revealed that the self-cleaning ability of lotus leaves and the striking ability of a water-strider’s legs to walk on water can be attributed to the ideal superhydrophobicity of their surfaces, induced by special microand nanostructures. To date, the biomimetic fabrication of superhydrophobic microand/or nanostructures has attracted considerable interest, and these types of materials can be used for such applications as self-cleaning coatings and stain-resistant textiles. Although a superhydrophobic technique inspired by lotus leaves is expected to be able to solve such fogging problems because the water droplets can not remain on the surface, there are no reports of such antifogging coatings. Very recently, researchers from General Motors have reported that the surfaces of lotus leaves become wet with moisture because the size of the fog drops are at the microscale—so small that they can be easily trapped in the interspaces among micropapillae. Thus, lotuslike surface microstructures are unsuitable for superhydrophobic antifogging coatings, and a new inspiration from nature is desired for solving this problem. In this communication, we report a novel, biological, superhydrophobic antifogging strategy. It was found that the compound eyes of the mosquito C. pipiens possess ideal superhydrophobic properties that provide an effective protective mechanism for maintaining clear vision in a humid habitat. Our research indicates that this unique property is attributed to the smart design of elaborate microand nanostructures: hexagonally non-close-packed (ncp) nipples at the nanoscale prevent microscale fog drops from condensing on the ommatidia surface, and hexagonally close-packed (hcp) ommatidia at the microscale could efficiently prevent fog drops from being trapped in the voids between the ommatidia. We also fabricated artificial compound eyes by using soft lithography and investigated the effects of microand nanostructures on the surface hydrophobicity. These findings could be used to develop novel superhydrophobic antifogging coatings in the near future. It is known that mosquitoes possess excellent vision, which they exploit to locate various resources such as mates, hosts, and resting sites in a watery and dim habitat. To better understand such remarkable abilities, we first investigated the interaction between moisture and the eye surface. An ultrasonic humidifier was used to regulate the relative humidity of the atmosphere and mimic a mist composed of numerous tiny water droplets with diameters less than 10 lm. As the fog was C O M M U N IC A IO N

The dry-style antifogging properties of mosquito compound eyes and artificial analogues prepared by soft lithography: a superhydrophobic state with high adhesive force

Microfluidics consist of microfabricated structures for liquid handling, with cross-sections in the 1–500 μm range, and small volume capacity (fL-nL) Capillary tubes connected with fittings,1 although utilizing small volumes, are not considered microfluidics for the purposes of this paper since they are not microfabricated Likewise, millifluidic systems, made by conventional machining tools, are excluded due to their larger feature sizes (>500 μm)

Though micromachined systems for gas chromatography were introduced in the 1970’s,2 the field of microfluidics did not gain much traction until the 1990’s3 Silicon and glass were the original materials used, but then the focus shifted to include polymer substrates, and in particular, polydimethylsiloxane (PDMS) Since then the field has grown to encompass a wide variety of materials and applications The successful demonstration of electrophoresis and electroosmotic pumping in a microfluidic device provided a nonmechanical method for both fluid control and separation4 Laser induced fluorescence (LIF) enabled sensitive detection of fluorophores or fluorescently labeled molecules The expanded availability of low-cost printing allowed for cheaper and quicker mask fabrication for use in soft lithography5 Commercial microfluidic systems are now available from Abbott, Agilent, Caliper, Dolomite, Micralyne, Microfluidic Chip Shop, Micrux Technologies and Waters, as a few prominent examples For a more thorough description of the history of microfluidics, we refer the reader to a number of comprehensive, specialized reviews,3, 6–11 as well as a more general 2006 review12

The field of microfluidics offers many advantages compared to carrying out processes through bulk solution chemistry, the first of which relates to a lesson taught to every first-year chemistry student Simply stated, diffusion is slow! Thus, the smaller the distance required for interaction, the faster it will be Smaller channel dimensions also lead to smaller sample volumes (fL-nL), which can reduce the amount of sample or reagents required for testing and analysis Reduced dimensions can also lead to portable devices to enable on-site testing (provided the associated hardware is similarly portable) Finally, integration of multiple processes (like labeling, purification, separation and detection) in a microfluidic device can be highly enabling for many applications

Microelectromechanical systems (MEMS) contain integrated electrical and mechanical parts that create a sensor or system Applications of MEMS are ubiquitous, including automobiles, phones, video games and medical and biological sensors13 Micro-total analysis systems, also known as labs-on-a-chip, are the chemical analogue of MEMS, as integrated microfluidic devices that are capable of automating multiple processes relevant to laboratory sciences For example, a typical lab-on-a-chip system might selectively purify a complex mixture (through filtering, antibody capture, etc), then separate target components and detect them

Microfluidic devices consist of a core of common components Areas defined by empty space, such as reservoirs (wells), chambers and microchannels, are central to microfluidic systems Positive features, created by areas of solid material, add increased functionality to a chip and can consist of membranes, monoliths, pneumatic controls, beams and pillars Given the ubiquitous nature of negative components, and microchannels in particular, we focus here on a few of their properties Microfluidic channels have small overall volumes, laminar flow and a large surface-to-volume ratio Dimensions of a typical separation channel in microchip electrophoresis (μCE) are: 50 μm width, 15 μm height and 5 cm length for a volume of 375 nL Flow in these devices is normally nonturbulent due to low Reynolds numbers For example, water flowing at 20°C in the above channel at 1 μL/min (222 cm/s) results in a Reynolds number of ~05, where <2000 is laminar flow Since flow is nonturbulent, mixing is normally diffusion-limited Small channel sizes also have a high surface-to-volume ratio, leading to different characteristics from what are commonly found in bulk volumes The material surface can be used to manipulate fluid movement (such as by electroosmotic flow, EOF) and surface interactions For a solution in contact with a charged surface, a double layer of charge is created as oppositely charged ions are attracted to the surface charges This electrical double layer consists of an inner rigid or Stern Layer and an outer diffuse layer An electrostatic potential known as the zeta potential is formed, with the magnitude of the potential decreasing as distance from the surface increases The electrical double layer is the basis for EOF, wherein an applied voltage causes the loosely bound diffuse layer to move towards an electrode, dragging the bulk solution along Charges on the exposed surface also exert a greater influence on the fluid in a channel as its size decreases Larger surface-to-volume ratios are more prone to nonspecific adsorption and surface fouling In particular, non-charged and hydrophobic microdevice surfaces can cause proteins in solution to denature and stick

We focus our review on advances in microfluidic systems since 2008 In doing this, we occasionally must cover foundational work in microfluidics that is considerably less recent We do not focus on chemical synthesis applications of microfluidics although it is an expanding area, nor do we delve into lithography, device fabrication or production costs Our specific emphasis herein is on four areas within microfluidics: properties and applications of commonly used materials, basic functions, integration, and selected applications For each of these four topics we provide a concluding section on opportunities for future development, and at the end of this review, we offer general conclusions and prospective for future work in the field Due to the considerable scope of the field of microfluidics, we limit our discussion to selected examples from each area, but cite in-depth reviews for the reader to turn to for further information about specific topics We also refer the reader to recent comprehensive reviews on advances in lab-on-a-chip systems by Arora et al10 and Kovarik et al14

/pdf/advances-in-microfluidic-materials-functions-integration-and-27mmao3n1o.pdf

Advances in microfluidic materials, functions, integration, and applications.

Separating blood plasma in microchannels is of great relevance to microfluidics-based biodetection However, the physics behind the separation of plasma from whole blood using acoustophoresis (movement driven by sound waves) is not well understood This study uses experiments and simulations to provide an improved understanding of plasma separation from whole blood using acoustophoresis It is seen that acoustophoretic focusing of cells depend on two time scales: that of shear-induced diffusion, and that of actual acoustophoresis These results will help in designing highly efficient blood-plasma separation devices for lab-on-a-chip applications

Improved Understanding of Acoustophoresis and Development of an Acoustofluidic Device for Blood Plasma Separation

We report capillary flow of blood in a microchannel with differential wetting for the separation of a plasma from sample blood and subsequent on-chip detection of glucose present in a plasma. A rectangular polydimethylsiloxane microchannel with hydrophilic walls (on three sides) achieved by using oxygen plasma exposure enables capillary flow of blood introduced at the device inlet through the microchannel. A hydrophobic region (on all four sides) in the microchannel impedes the flow of sample blood, and the accumulated blood cells at the region form a filter to facilitate the separation of a plasma. The modified wetting property of the walls and hence the device performance could be retained for a few weeks by covering the channels with deionised water. The effects of the channel cross-section, exposure time, waiting time, and location and length of the hydrophobic region on the volume of the collected plasma are studied. Using a channel cross-section of 1000 × 400 μm, an exposure time of 2 min, a waiting time of 10 min, and a hydrophobic region of width 1.0 cm located at 10 mm from the device inlet, 450 nl of plasma was obtained within 15 min. The performance of the device was found to be unaffected (provides 450 nl of plasma in 15 min) even after 15 days. The purification efficiency and plasma recovery of the device were measured and found to be comparable with that obtained using the conventional centrifugation process. Detection of glucose at different concentrations in whole blood of normal and diabetic patients was performed (using 5 μl of sample blood within 15 min) to demonstrate the compatibility of the device with integrated detection modules.

/pdf/capillary-flow-of-blood-in-a-microchannel-with-differential-1vv4iatg28.pdf

Capillary flow of blood in a microchannel with differential wetting for blood plasma separation and on-chip glucose detection

We report the capillary flow enhancement in rectangular polymer microchannels, when one of the channel walls is a deformable polymer membrane. We provide detailed insight into the physics of elastocapillary interaction between the capillary flow and elastic membrane, which leads to significant improvements in capillary flow performance. As liquid flows by capillary action in such channels, the deformable wall deflects inwards due to the Young-Laplace pressure drop across the liquid meniscus. This, in turn, decreases the radius of curvature of the meniscus and increases the driving capillary pressure. A theoretical model is proposed to predict the resultant increase in filling speed and rise height, respectively, in deformable horizontal and vertical microchannels having large aspect ratios. A non-dimensional parameter $J$, which represents the ratio of the capillary force to the mechanical restoring force, is identified to quantify the elastocapillary effects in terms of the improvement in filling speed (for $Jg0.238$) and the condition for channel collapse ($Jg1$). The theoretical predictions show good agreement with experimental data obtained using deformable rectangular poly(dimethylsiloxane) microchannels. Both model predictions and experimental data show that over 15% improvement in the Washburn coefficient in horizontal channels, and over 30% improvement in capillary rise height in vertical channels, are possible prior to channel collapse. The proposed technique of using deformable membranes as channel walls is a viable method for capillary flow enhancement in microfluidic devices.

Capillary flow enhancement in rectangular polymer microchannels with a deformable wall.

This work presents a study of a passive micromixer with lateral obstructions along a microchannel. The mixing process is simulated by solving the continuity, momentum and diffusion equations. The mixing performance is quantified in terms of a parameter called ‘mixing efficiency’. A comparison of mixing efficiencies with and without obstructions clearly indicates the benefit of having obstructions along the microchannel. The numerical model was validated by comparing simulation results with experimental results for a micromixer. An extensive parametric study was carried out to investigate the influence of the geometrical and operational parameters in terms of the mixing efficiency and pressure drop, which are two important criteria for the design of micromixers. A very interesting observation reveals that there exists a critical Reynolds number (Re
 cr
  ~ 100) below which the mixing process is diffusion dominated and thus the mixing efficiency is reduced with increase in Re and above which the mixing process is advection dominated and mixing efficiency increases with increase in Re. Microchannels with symmetric and staggered protrusion arrangements were studied and compared. The mixing performance of the staggered arrangement was comparable with that of symmetric arrangement but the pressure drop was lower in the case of staggered arrangements making it more suitable.

Investigations into mixing of fluids in microchannels with lateral obstructions

We report irreversible Cassie–Wenzel wetting transition on a nanostructured superhydrophobic surface employing surface acoustic wave (SAW) vibration. The transition is achieved upon penetration of the liquid into the nanogrooves driven by the inertial energy of the drop imparted by the SAW. However, the filling up of nanopores imposes an energy barrier ( E b) to the transition, which requires the displacement of the initial solid–air interface inside the pores with a solid–liquid interface. We unravel that the relative magnitudes of the input acoustic energy ( E a c), and this energy barrier, hence, dictate the occurrence of the wetting transition, with the irreversibility in the transition, therefore, being explained from energy minimization of the system following the transition. In addition, observing the dynamics of the wetting front allowed the different regimes of the wetting transition process to be identified.

Ashis Kumar Sen

Papers

Improved Understanding of Acoustophoresis and Development of an Acoustofluidic Device for Blood Plasma Separation

Capillary flow of blood in a microchannel with differential wetting for blood plasma separation and on-chip glucose detection

Capillary flow enhancement in rectangular polymer microchannels with a deformable wall.

Investigations into mixing of fluids in microchannels with lateral obstructions

Cassie-Wenzel wetting transition on nanostructured superhydrophobic surfaces induced by surface acoustic waves