Integrated microfluidic devices with enhanced separation performance: Application to phosphoproteome analyses of differentiated cell model systems

On-line pre-treatment, separation, and nanoelectrospray mass spectrometric determinations for pesticide metabolites and peptides based on a modular microfluidic platform

In order to address time-consuming sample pre-treatment and separation prior to mass spectrometry (MS) identifications, highly integrated chips were developed, but damage to any functional unit in these chips would result in complete replacement. Herein, we propose a modular microfluidic platform comprising pre-treatment, liquid chromatography (LC) separation and nanoelectrospray ionization (nESI) chips for on-line enrichment, separation and nESI MS detection of pesticide metabolites and peptides. The pre-treatment chip is applicable in enriching pyridalyl and its metabolites, and it achieves optimal desalination efficiency, 98.5%, for polymerase chain reaction products. Additionally, the LC separation chip was fully characterised, and it demonstrated satisfactory separation efficiency, quantification ability and pressure durability. Finally, the modular microfluidic platform was used to identify the peptides in trypsin-digested casein. Four additional peptides were identified, indicating an improvement in detection ability compared with using off-line zip tips coupled with MS investigations. Because the proposed modular platform can significantly reduce manual work, it would be a potential tool to achieve high throughput and automatic MS identifications with low sample consumptions.

A microfluidic platform, composed of enrichment, separation and nanoelectrospray ionization modulations was developed to on-line-investigate pesticide metabolites and peptides.

Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics

Comprehensive proteomic profiling of biological specimens usually requires multidimensional chromatographic peptide fractionation prior to mass spectrometry. However, this approach can suffer from poor reproducibility because of the lack of standardization and automation of the entire workflow, thus compromising performance of quantitative proteomic investigations. To address these variables we developed an online peptide fractionation system comprising a multiphasic liquid chromatography (LC) chip that integrates reversed phase and strong cation exchange chromatography upstream of the mass spectrometer (MS). We showed superiority of this system for standardizing discovery and targeted proteomic workflows using cancer cell lysates and nondepleted human plasma. Five-step multiphase chip LC MS/MS acquisition showed clear advantages over analyses of unfractionated samples by identifying more peptides, consuming less sample and often improving the lower limits of quantitation, all in highly reproducible, automated, online configuration. We further showed that multiphase chip LC fractionation provided a facile means to detect many N- and C-terminal peptides (including acetylated N terminus) that are challenging to identify in complex tryptic peptide matrices because of less favorable ionization characteristics. Given as much as 95% of peptides were detected in only a single salt fraction from cell lysates we exploited this high reproducibility and coupled it with multiple reaction monitoring on a high-resolution MS instrument (MRM-HR). This approach increased target analyte peak area and improved lower limits of quantitation without negatively influencing variance or bias. Further, we showed a strategy to use multiphase LC chip fractionation LC-MS/MS for ion library generation to integrate with SWATH(TM) data-independent acquisition quantitative workflows. All MS data are available via ProteomeXchange with identifier PXD001464.

Chip-based nanoflow high performance liquid chromatography coupled to mass spectrometry for profiling of soybean flavonoids

In this work a chip-based nano HPLC coupled MS (HPLC-chip/MS) method with a simple sample preparation procedure was developed for the flavonoid profiling of soybean. The analytical properties of the method including the linearity (R(2) , 0.992-0.995), reproducibility (RSD, 1.50-7.66%), intraday precision (RSD, 1.41-5.14%) and interday precision (RSD, 2.76-16.90%) were satisfactory. Compared with the conventional HPLC/MS method, a fast extraction and analysis procedure was applied and more flavonoids were detected in a single run. Additionally, 13 flavonoids in soybean seed were identified for the first time. The method was then applied to the profiling of six varieties of soybean sowed at the same place. A clear discrimination was observed among different cultivars, three isoflavones, accounting for nearly 80% of total flavonoid contents, were found increased in the spring soybeans compared with the summer cultivars.

An overview of recent advances in HPLC instrumentation

This review highlights the fundamentals and the most prominent advances in the field of HPLC instrumentation over the last decades. Fundamental aspects and practical considerations of column switching, conventional (heart-cut) and comprehensive two-dimensional LC are presented. Different aspects of microcolumn- and nanoliquid-chromatography are reviewed. Recent progress in column technology and the demands and developments in instrumentation and accessories for miniaturized LC are also discussed. In the field of miniaturization, particularly in chip-based nano-LC systems, some aspects on micro-fluidic chip fabrication, using particle-packed HPLC microchips or polymer-based monoliths, are addressed. An introduction to ultra performance LC (UPLC) is also presented.

Comparison of liquid chromatography-microchip/mass spectrometry to conventional liquid chromatography-mass spectrometry for the analysis of steroids

The feasibility of a microfluidic-based liquid chromatography-electrospray ionization/mass spectrometric system (HPLC-Chip/ESI/MS) was studied and compared to a conventional narrow-bore liquid chromatography-electrospray ionization/mass spectrometric (LC-ESI/MS) system for the analysis of steroids. The limits of detection (LODs) for oxime derivatized steroids, expressed as concentrations, were slightly higher with the HPLC-Chip/MS system (50-300 pM) using an injection volume of 0.5 μL than with the conventional LC-ESI/MS (10-150 pM) using an injection volume of 40 μL. However, when the LODs are expressed as injected amounts, the sensitivity of the HPLC-Chip/MS system was about 50 times higher than with the conventional LC-ESI/MS system. The results indicate that the use of HPLC-Chip/MS system is clearly advantageous only in the analysis of low-volume samples. Both methods showed good linearity and good quantitative and chromatographic repeatability. In addition to the instrument comparisons with oxime derivatized steroids, the feasibility of the HPLC-Chip/MS system in the analysis of non-derivatized and oxime derivatized steroids was compared. The HPLC-Chip/MS method developed for non-derivatized steroids was also applied to the quantitative analysis of 15 mouse plasma samples.

Microfluidics in protein chromatography

The development of microfluidics and its utilization in a myriad of applications has grown exponentially over the past 15 years. One area that has benefited from the great strides in fabrication of microelectromechanical systems (MEMS) is separations chemistry. Most studies have focused on small molecule and DNA separations; few on protein chromatographic techniques on microchips. This review details recent developments in protein separations on microfluidic platforms and how MEMS have the potential for revolutionizing protein chromatography.

Monolithic porous polymer stationary phases in polyimide chips for the fast high-performance liquid chromatography separation of proteins and peptides

Poly(lauryl methacrylate-co-ethylene dimethacrylate) and poly(styrene-co-divinylbenzene) stationary phases in monolithic format have been prepared by thermally initiated free radical polymerization within polyimide chips featuring channels having a cross-section of 200micromx200microm and a length of 6.8cm. These chips were then used for the separation of a mixture of proteins including ribonuclease A, myoglobin, cytochrome c, and ovalbumin, as well as peptides. The separations were monitored by UV adsorption. Both the monolithic phases based on methacrylate and on styrene chemistries enabled the rapid baseline separation of most of the test mixtures. Best performance was achieved with the styrenic monolith leading to fast baseline separation of all four proteins in less than 2.5min. The in situ monolith preparation process affords microfluidic devices exhibiting good batch-to-batch and injection-to-injection repeatability.

Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins

The post-translational modification (PTM) of proteins is a common biological mechanism for regulating protein localization, function, and turnover. The direct analysis of modifications is required because they are not coded by genes, and thus are not predictable. Different MS-based proteomic strategies are used for the analysis of PTMs, such as phosphorylation and glycosylation, and are composed of a structural simplification step of the protein followed by specific isolation step to extract the classes of modified peptides (also called "sub-proteomes") before mass spectrometry. This specific isolation step is necessary because PTMs occur at a sub-stoichiometric level and signal suppression of the modified fractions in the mass spectrometer occurs in the presence of the more-abundant non-modified counterpart. The request of innovative analytical strategies in PTM studies is the capability to localize the modification sites, give detailed structural information on the modification, and determine the isoform composition with increased selectivity, sensitivity, and throughput. This review focuses on the description of recent integrated analytical systems proposed for the analysis of PTMs in proteins, and their application to profile the glycoproteome and the phosphoproteome in biological samples. Comments on the difficulties and usefulness of the analytical strategies are given.

A brief summary of the different types of mass spectrometers used in proteomics

Recent technical innovations in mass spectrometry-based techniques have resulted in a range of highly sensitive and versatile instruments for high-throughput, high-sensitive, proteome-scale profiling. This wide diversity of instrumentation commercially available for mass spectrometry-based proteomics makes the choice of instrumentation sometimes difficult. The choice of instruments depends on the biological problem and the proteomic strategy chosen for protein identification. This chapter will give a short overview of the instruments routinely used in proteomic laboratories and the technical criteria that should be considered before instrument selection.

Chip-based nano-LC-MS/MS identification of proteins in complex biological samples using a novel polymer microfluidic device

Although the proteome of each organism is unambiguously coded in its genome, the proteome shows the real biology in action in each particular organism. New powerful tools are being developed for biochemists and biologists to analyze complex biological samples for studying the complete protein supplement of the genome, i. e., the proteome. There are several methods available for proteome analysis including 2-DE and several forms of MS. In recent years, technologies such as microfluidics and array-based systems have appeared in the field of analysis, identification, and quantification of proteins. These novel approaches might help in solving current technical challenges in proteomics. This paper presents a practical application of the first commercially available microfluidic nano-ESI device coupled with nano-LC (i. e., HPLC-chip) for the analysis of samples of some biological protein mixtures.

A decade of microfluidic analysis coupled with electrospray mass spectrometry: an overview

This review presents a thorough overview covering the period 1997-2006 of microfluidic chips coupled to mass spectrometry through an electrospray interface. The different types of fabrication processes and materials used to fabricate these chips throughout this period are discussed. Three 'eras' of interfaces are clearly distinguished. The earliest approach involves spraying from the edge of a chip, while later devices either incorporate a standard fused-silica emitter inserted into the device or fully integrated emitters formed during chip fabrication. A summary of microfluidic-electrospray devices for performing separations and sample pretreatment steps before sample introduction into the mass spectrometer is also presented.

Analytical performance of a venturi-assisted array of micromachined ultrasonic electrosprays coupled to ion trap mass spectrometry for the analysis of peptides and proteins

The analytical characterization of a novel ion source for mass spectrometry named array of micromachined ultrasonic electrosprays (AMUSE) is presented here. This is a fundamentally different type of ion generation device, consisting of three major components: (1) a piezoelectric transducer that creates ultrasonic waves at one of the resonant frequencies of the sample-filled device, (2) an array of pyramidally shaped nozzles micromachined on a silicon wafer, and (3) a spacer which prevents contact between the array and transducer ensuring the transfer of acoustic energy to the sample. A high-pressure gradient generated at the apexes of the nozzle pyramids forces the periodic ejection of multiple droplet streams from the device. With this device, the processes of droplet formation and droplet charging are separated; hence, the limitations of conventional electrospray-type ion sources, including the need for high charging potentials and the addition of organic solvent to decrease surface tension, can be avoided. In this work, a Venturi device is coupled with AMUSE in order to increase desolvation, droplet focusing, and signal stability. Results show that ionization of model peptides and small tuning molecules is possible with dc charging potentials of 100 Vdc or less. Ionization in rf-only mode (without dc biasing) was also possible. It was observed that, when combined with AMUSE, the Venturi device provides a 10-fold gain in signal-to-noise ratio for 90% aqueous sample solutions. Further reduction in the diameter of the orifices of the micromachined arrays led to an additional signal gain of at least 3 orders of magnitude, a 2-10-fold gain in the signal-to-noise ratio and an improvement in signal stability from 47% to 8.5% RSD. The effectiveness of this device for the soft ionization of model proteins in aqueous media, such as cytochrome c, was also examined, yielding spectra with an average charge state of 8.8 when analyzed with a 100 Vdc charging potential. Ionization of model proteins was also possible in rf-only mode.

The fundamental aspects and applications of Agilent HPLC-Chip

It has been over 3 years since the first publication of the polymer microfluidic HPLC-Chip technology and more than 1 year since this technology became commercially available. Here, we summarize the design principle and fabrication processes of the Agilent HPLC-Chip and review the applications published so far.

Microfluidic chip-based protein capture from human whole blood using octadecyl (C18) silica beads for nucleic acid analysis from large volume samples

We have previously described the development of a novel capillary-based photopolymerized monolith that offered unprecedented efficiency (approximately 85%) for DNA extraction from pre-purified human genomic DNA [J. Wen, C. Guillo, J.P. Ferrance, J.P. Lander, Anal. Chem. 78 (2006) 1673]. However, the major drawback associated with this phase was the limited binding capacity and low extraction efficiency (<40%) when purifying nucleic acids from a volume of whole blood greater than 0.1 microL. The limited DNA binding capacity, hypothesized to result from an overwhelming mass of protein overloading the monolith phase, severely limits the clinical utility, which will require a whole blood DNA capacity orders of magnitude larger. One proposed solution involved use of a protein capture bed to remove the majority of the protein present in blood before nucleic acid extraction was performed. To evaluate this, microchips with different channel configurations were designed and tested containing silica beads with various reversed phases, and their protein capture efficiency determined. Triton X-100 in the cell lysis buffer was found to be a critical component, greatly affecting the binding of proteins to the C18 reversed phase. An optimum Triton X-100 concentration of 0.1% was determined to enhance red and white blood cell lysis without adversely affecting protein binding to the C18 phase. A parallel 4-chamber design was found to be optimal, with 70% of the proteins (1020+/-45 microg) from a load solution containing 10 microL of whole blood captured on the C18 phase in a single microdevice. Electrophoretic analysis of the proteins in the flow-through of the C18 phase showed the absence of hemoglobin and larger proteins/peptides, indicating that they had been captured by the C18 phase, preventing these polymerase chain reaction inhibitory proteins from reaching and binding to the subsequent matrix which would be used for DNA capture.

A virtual valve for smooth contamination-free flow switching

We present a channel geometry that allows for clean switching between different inlets of a microchip without any contamination of the inlets or the downstream flow. We drive this virtual valve with a pneumatic pressure setup that minimizes disturbance of the downstream flow during the switching procedure by simultaneous variation of the pressures applied to the different inlets. We assess the efficiency of the setup by spectroscopic measurement of downstream dye concentrations, and demonstrate its practical utility by sequentially constructing multiple layers of alginate hydrogel. The method is potentially useful for a whole series of further applications, such as changing perfusion liquids for cell culture and cell analysis, metering, chemical-reaction initiation and multi-sample chromatography, to name a few.

Recent applications in nanoliquid chromatography

Since its first introduction by Karlsson and Novotny in 1988 nano-LC has emerged as a complementary and/or competitive separation method to conventional HPLC, offering several advantages such as higher efficiency, ability to work with minute sample sizes and lower consumption of mobile phases, and better compatibility with MS, etc. Although its use was not so extended initially, in the last years new and interesting applications have appeared which deserve to be carefully considered. The aim of this review is therefore to provide an updated and critical survey of different nano-LC applications in analytical chemistry.

Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease

Novel approaches for the qualitative and quantitative proteomics analysis by nanoscale LC-MS applied to the study of protein expression response in depleted and undepleted serum of Gaucher patients undergoing enzyme replacement therapy are presented. Particular emphasis is given to the method reproducibility of these LC-MS experiments without the use of isotopic labels. The level of chitotriosidase, an established Gaucher biomarker, was assessed by means of an absolute concentration determination technique for alternate scanning LC-MS generated data. Disease associated proteins, including fibrinogens, complement cascade proteins, and members of the high density lipoprotein serum content, were recognized by various clustering methods and sorting and intensity profile grouping of identified peptides. Condition-unique LC-MS protein signatures could be generated utilizing the measured serum protein concentrations and are presented for all investigated conditions. The clustering results of the study were also used as input for gene ontology searches to determine the correlation between the molecular functions of the identified peptides and proteins.

Miniaturization: Chip-based liquid chromatography and proteomics

Proteomic research is linked with significant technological challenges such as the high dynamic range and low abundance of biologically interesting proteins. Moreover, there is an increasing need for high-throughput and robustness of routinely performed analyses. Solving these difficulties requires refinements in the capability to fractionate and prepare biological samples as well as improvements in speed, automation, separation power and overall analytical sensitivity.Recent innovations in microfluidic devices with integrated on-chip sample enrichment, liquid chromatography and electrospray emitters and their applicability for specific proteomic applications are presented in this review.: