Simple fabrication of hydrophobic surface target for increased sensitivity and homogeneity in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of peptides,phosphopeptides, carbohydrates and proteins

To enhance sample signals and improve homogeneity in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, a simple, rapid, and efficient sample preparation method was developed in this study. Polydimethylsiloxane (PDMS) was coated on a stainless steel MALDI plate, forming a transparent, hydrophobic surface that enhanced sample signals without producing observable background signals. Compared to the use of an unmodified commercial metal MALDI plate, peptide signals were enhanced by ~7.1–11.0-fold due to the reduced sample spot area of the PDMS-coated plate, and showed improved peptide mass fingerprinting (PMF) and MS/MS peptide sequencing results. In the analysis of phosphopeptides and carbohydrates with a 2,5-dihydroxybenzoic acid (DHB) matrix, the PDMS-coated plate showed improved sample homogeneity and signal enhancements of ~5.2–8.2-fold and ~2.8–3.2-fold, respectively. Improved sensitivity in the observation of more unique fragment ions by MS/MS analysis, to successfully distinguish isomeric carbohydrates, was also illustrated. In protein analysis with a sinapinic acid (SA) matrix, a ~3.4-fold signal enhancement was observed. The PDMS film coating was easily removed and refabricated to avoid sample carryover, and was applicable to diverse commercial MALDI plates. The PDMS-coated approach is a simple, practical, and attractive method for enhancing analyte signals and homogeneity.     

Stable photochromism and controllable reduction properties of surfactant-encapsulated polyoxometalate/silica hybrid films

In this paper, we present a novel strategy for fabricating polyoxometalate (POM)-based photochromic silica hybrid films. To combine metal nanoparticles (NPs) into the POMs embedded silica matrix, furthermore, we realized the controllable in situ synthesis of metal NPs in the film by utilizing the reduction property of POMs existing in the reduced state. Through electrostatic encapsulation with hydroxyl-terminated surfactants, the POMs with good redox property can be covalently grafted onto a silica matrix by means of a sol-gel approach, and stable silica sol-gel thin films containing surfactant-encapsulated POMs can be obtained. The functional hybrid film exhibits both the transparent and easily processible properties of silica matrix and the stable and reversible photochromism of POMs. In addition, well-dispersed POMs in a hydrophobic microenvironment within the hybrid film can be used as reductants for the in situ synthesis of metal NPs. More significantly, the size and location of NPs can be tuned by controlling the adsorption time of metal ions and mask blocking the surface. The hybrid film containing both POMs and metal NPs with patterned morphology can be obtained, which has potential applications in optical display, memory, catalysis, microelectronic devices and antibacterial materials.     

A sample preparation method for recovering suppressed analyte ions in MALDI TOF MS

In matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS), analyte signals can be substantially suppressed by other compounds in the sample. In this technical note, we describe a modified thin‐layer sample preparation method that significantly reduces the analyte suppression effect (ASE). In our method, analytes are deposited on top of the surface of matrix preloaded on the MALDI plate. To prevent embedding of analyte into the matrix crystals, the sample solution were prepared without matrix and efforts were taken not to re‐dissolve the preloaded matrix. The results with model mixtures of peptides, synthetic polymers and lipids show that detection of analyte ions, which were completely suppressed using the conventional dried‐droplet method, could be effectively recovered by using our method. Our findings suggest that the incorporation of analytes in the matrix crystals has an important contributory effect on ASE. By reducing ASE, our method should be useful for the direct MALDI MS analysis of multicomponent mixtures. Copyright © 2015 John Wiley & Sons, Ltd.     

Multisample preparation methods for the solvent-free MALDI-MS analysis of synthetic polymers

A limitation of any current approach using solvent-free MALDI mass spectrometry is that only one sample at a time can be prepared and transferred to the MALDI-plate. For this reason, multiple-sample preparation approaches for solvent-free MALDI MS analysis of synthetic polymers were developed that are simple and practical. One approach multiplexed sample preparation by simultaneously preparing multiple samples. With this approach, as many as 384 samples could be prepared by addition of analyte, matrix, salt, and 1-mm metal beads to each well of a 384-well disposable bacti plate, capping the plate with the lid and homogenizing all samples simultaneously using a common laboratory vortex device. Besides the time savings achieved by a single vortex step for multiple samples, an additional advantage of this method relative to previously reported solvent-free preparation methods is that the mixing volume per sample is reduced, which allows a reduction in the amount of analyte required. This method, however, still requires the transfer of each homogenized sample to the MALDI plate for subsequent analysis. Here we report a novel approach that combines multiple simultaneous solvent-free sample preparation with automatic sample transfer to the MALDI target plate. This approach reduces the possibility of cross-contamination, the amount of sample and matrix consumed for an analysis, and the time required for preparation of multiple samples. These methods were shown to provide high-quality mass spectra for various synthetic polymer standards with M(n) values to 10 kDa. The methods are efficient in that small sample amounts are required, the sample/salt/matrix ratio is not critical, and the time necessary to achieve sufficient homogenization of multiple samples is less than 5 min.     

Monitoring the redox cycle of low-molecular peptides using a modified target plate in MALDI-MS

A new method is being proposed for preparing MALDI target plates with a hydrophobic polymer coating and hydrophilic anchors. The particles of the MALDI matrix were pre-mixed with a poly[4,5-difluoro-2,2-bis(trifluoromethyl)-1,3-dioxole-co-tetrafluoroethylene] solution prior to their placement on a mass-spectrometric sample support. This technique led to the formation of matrix microspots with a diameter of less than 1 mm inside the polymer. The polymer and matrix concentration as well as the amount of suspension placed on the target plate influenced the size and quality of microspots to a great extent. The sensitivity of the mass-spectrometric analysis was confirmed by obtaining the mass spectra of fmole concentrations of an apomyoglobin tryptic digest. The potential proteomic application of this type of MALDI surface preparation was demonstrated by performing the redox cycle using glutathione and its analogue. All reactions were carried out directly on a MALDI plate, which accommodates low volumes of reagents and prevents sample loss.     

Sol-Gel as Reaction Matrix for Bacterial Enzymatic Activity

Sol-gel process is a rapid growing field in material chemistry. The sol-gel matrices (SGM) are basically porous wet-gels or xerogels obtained by the hydrolysis and condensation-polymerisation of metal and semimetal alkoxides, mainly SiO₂ materials. The current study presents the uses of sol-gel glass matrix (SGM) that allow direct entrapment of biomolecules within and at surface, which can be utilized by microorganisms. This glass type is solid, transparent, porous and can be modulated to form a hydrophobic or hydrophilic surface. In view of all these beneficial characteristics of SGM, preliminary data is presented on biofilm formed on thin films of SGM doped with a fluorochrome (fluorescein diacetate). The esterase/lipase activity of E. coli CN ₁₃ and K. oxytoca spp. biofilm grown on top of SGM thin film, doped with fluorescein diacetate, was detected at the level of a single cell by epifluorescence microscopy. In view of these preliminary results, sol-gel glass has a considerable potential as a variable matrix for single bacteria and biofilm investigation.     

Graphite Supported Preparation (GSP) of α-Cyano-4-Hydroxycinnamic Acid (CHCA) for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) for Peptides and Proteins

Graphite as MALDI matrix or in combination with other substances has been reported in recent years. Here, we demonstrate that graphite can be used as target coating supporting the crystallization of the ??-cyano-4-hydroxycinnamic acid matrix. A conventional dried-droplet preparation of matrix and analyte solution on a graphite-coated metal target leads to a thin, uniform layer of cubic crystals with about 1???m edge length. Commercially available graphite powder of 1?C2???m particle size is gently wiped over the target using a cotton Q-tip, leading to an ultra-thin, not-visible film. This surface modification considerably improves analysis of peptides and proteins for MALDI MS using conventional dried-droplet preparation. Compared with untreated targets, the signal intensities of standard peptides are up to eight times higher when using the graphite supported crystallization. The relative standard deviation in peak area of angiotensin II for sample amounts between 1 and 50?fmol is reduced to about 15?% compared with 45?% for untreated sample holders. For a quantification of 1?fmol of the peptide using an internal standard the coefficient of variation is reduced to 3.5?% from 8?%. The new graphite supported preparation (GSP) protocol is very simple and does not require any technical nor manual skills. All standard solvents for peptides and proteins can be used.     

Nanocrystalline Diamond Thin Films Synthesis on Curved Surface

Thin films of curved surface nanocrystalline diamond (CS-NCD) are a category of important materials. However, the development of such materials is still a highly challenging task. Here we present a novel approach to synthesizing CS-NCD thin films deposited on non-spherical surfaces of molybdenum substrate using direct current plasma jet chemical vapor deposition. A special cooling system was designed and applied to ensure uniform substrate temperature. It is demonstrated from simulation and experimental results that this system is favorable for the production of thin films. The results show that the quality of CS-NCD thin films depends on the selection of optimal values of parameters including CH₄ concentration, substrate temperature, and chamber pressure. If the CH₄ concentration and/or the substrate temperature is too high or low, it results in non-diamond phase or micron-crystalline diamond thin films. Synthetic CS-NCD thin films using the proposed method have a smooth surface and uniform thickness. The average grain size and the mean surface roughness are approximately 30 and 4.3 nm respectively. Characteristics of CS-NCD thin film spectra comprised of the full width at half maximum with broad Raman peaks around 1,140 and 1,480 cm^?1, confirming the presence of the NCD phase.     

Silver Nanoparticle Thin Films with Nanocavities for Surface‐Enhanced Raman Scattering

The formation of nanometer‐sized gaps between silver nanoparticles is critically important for optimal enhancement in surface‐enhanced Raman scattering (SERS). A simple approach is developed to generate nanometer‐sized cavities in a silver nanoparticle thin film for use as a SERS substrate with extremely high enhancement. In this method, a submicroliter volume of concentrated silver colloidal suspension stabilized with cetyltrimethylammonium bromide (CTAB) is spotted on hydrophobic glass surfaces prepared by the exposure of the glass to dichloromethysilane vapors. The use of a hydrophobic surface helps the formation of a more uniform silver nanoparticle thin film, and CTAB acts as a molecular spacer to keep the silver nanoparticles at a distance. A series of CTAB concentrations is investigated to optimize the interparticle distance and aggregation status. The silver nanoparticle thin films prepared on regular and hydrophobic surfaces are compared. Rhodamine 6G is used as a probe to characterize the thin films as SERS substrates. SERS enhancement without the contribution of the resonance of the thin film prepared on the hydrophobic surface is calculated as 2×10⁷ for rhodamine 6G, which is about one order of magnitude greater than that of the silver nanoparticle aggregates prepared with CTAB on regular glass surfaces and two orders of magnitude greater than that of the silver nanoparticle aggregates prepared without CTAB on regular glass surfaces. A hydrophobic surface and the presence of CTAB have an increased effect on the charge‐transfer component of the SERS enhancement mechanism. The limit of detection for rhodamine 6G is estimated as 1.0×10^?8 M . Scanning electron microscopy and atomic force microscopy are used for the characterization of the prepared substrate.     

Novel approach to enhance sensitivity in surface‐assisted laser desorption/ionization mass spectrometry imaging using deposited organic‐inorganic hybrid matrices

Sample pretreatment is key to obtaining good data in matrix‐assisted laser desorption/ionization mass spectrometry imaging (MALDI‐MSI). Although sublimation is one of the best methods for obtaining homogenously fine organic matrix crystals, its sensitivity can be low due to the lack of a solvent extraction effect. We investigated the effect of incorporating a thin film of metal formed by zirconium (Zr) sputtering into the sublimation process for MALDI matrix deposition for improving the detection sensitivity in mouse liver tissue sections treated with olanzapine. The matrix‐enhanced surface‐assisted laser desorption/ionization (ME‐SALDI) method, where a matrix was formed by sputtering Zr to form a thin nanoparticle layer before depositing MALDI organic matrix comprising α‐cyano‐4‐hydroxycinnamic acid (CHCA) by sublimation, resulted in a significant improvement in sensitivity, with the ion intensity of olanzapine being about 1800 times that observed using the MALDI method, comprising CHCA sublimation alone. When Zr sputtering was performed after CHCA deposition, however, no such enhancement in sensitivity was observed. The enhanced sensitivity due to Zr sputtering was also observed when the CHCA solution was applied by spraying, being about twice as high as that observed by CHCA spraying alone. In addition, the detection sensitivity of these various pretreatment methods was similar for endogenous glutathione. Given that sample preparation using the ME‐SALDI‐MSI method, which combines Zr sputtering with the sublimation method for depositing an organic matrix, does not involve a solvent, delocalization problems such as migration of analytes observed after matrix spraying and washing with aqueous solutions as sample pretreatment are not expected. Therefore, ME‐Zr‐SALDI‐MSI is a novel sample pretreatment method that can improve the sensitivity of analytes while maintaining high spatial resolution in MALDI‐MSI.     

Increasing sensitivity and decreasing spot size using an inexpensive, removable hydrophobic coating for matrix-assisted laser desorption/ionisation plates

Spot size reduction and increased detection sensitivity in matrix-assisted laser desorption/ionisation (MALDI) of small molecules are accomplished by using an inexpensive and removable hydrophobic coating for MALDI targets, based on 3M Scotch Gard surface treatment. Several variations in sample preparation were explored, such as surface coating technique, identity of the matrix, solvent composition, and the type of metal support plate used. These were investigated on both uncoated and coated surfaces and their impact on spot size, crystal coverage, and sensitivity is presented here. Additionally, crystallisation behaviour obtained on coated plates is compared with that on uncoated plates using scanning electron microscope analysis. To demonstrate the potential of the new coating technique, erythromycin A and valinomycin are studied to determine the increase in detection sensitivity of coated plates in comparison to uncoated plates, and to reveal the suitability of the plates for application in combined high-performance liquid chromatography/MALDI (HPLC/MALDI), where widely varying solvent compositions and droplet volumes are observed. It is shown that enhancements in detection sensitivities correlate very well with the achieved spot size reduction. The versatility of the coated plates is also exhibited by the ease of removing the surface layer, after which the plates can be rigorously cleaned without worry about damaging the hydrophobic surface, followed by a quick reapplication of new hydrophobic coating material. This makes the non-polar coating superior to more expensive commercial hydrophobic-coated targets, which are much more delicate to clean. Furthermore, cleaning and reapplication eliminate potential carry-over effects and the easy application procedure also makes the fabrication of inexpensive, disposable MALDI targets readily possible.     

Langmuir films of flexible polymers transferred to aqueous/liquid crystal interfaces induce uniform azimuthal alignment of the liquid crystal

We reported recently that amphiphilic polymers can be assembled at interfaces created between aqueous phases and thermotropic liquid crystals (LCs) in ways that: (i) couple the organization of the polymer to the order of the LC and (ii) respond to changes in the properties of aqueous phases that can be characterized as changes in the optical appearance of the LC. This investigation sought to characterize the behavior of aqueous–LC interfaces decorated with uniaxially compressed thin films of polymers transferred by Langmuir–Schaefer (LS) transfer. Here, we report physicochemical characterization of interfaces created between aqueous phases and the thermotropic LC 4-cyano-4′-pentylbiphenyl (5CB) decorated with Langmuir films of a novel amphiphilic polymer (polymer 1), synthesized by the addition of hydrophobic and hydrophilic side chains to poly(2-vinyl-4,4′-dimethylazlactone). Initial characterization of this system resulted in the unexpected observation of uniform azimuthal alignment of 5CB after LS transfer of the polymer films to aqueous–5CB interfaces. This paper describes characterization of Langmuir films of polymer 1 hosted at aqueous–5CB interfaces as well as the results of our investigations into the origins of the uniform ordering of the LC observed upon LS transfer. Our results, when combined, support the conclusion that uniform azimuthal alignment of 5CB is the result of long-range ordering of polymer chains in the Langmuir films (in a preferred direction orthogonal to the direction of compression) that is generated during uniaxial compression of the films prior to LS transfer. Although past studies of Langmuir films of polymers at aqueous–air interfaces have demonstrated that in-plane alignment of polymer backbones can be induced by uniaxial compression, these past reports have generally made use of polymers with rigid backbones. One important outcome of this current study is thus the observation of anisotropy and long-range order in Langmuir films of a novel flexible polymer. A second important outcome is the observation that the existence, extent, and dynamics of this order can be identified and characterized optically by transfer of the Langmuir film to a thin film of LC. Additional characterization of Langmuir films of two other flexible polymers [poly(methyl methacrylate) and poly(vinyl stearate)] using this method also resulted in uniform azimuthal alignment of 5CB, suggesting that the generation of long-range order in uniaxially compressed Langmuir films of polymers may also occur more generally over a broader range of polymers with flexible backbones.     

Ready-made matrix-assisted laser desorption/ionization target plates coated with thin matrix layer for automated sample deposition in high-density array format.

The methodology for ready-made matrix-assisted laser desorption/ionization (MALDI) target plates covered with an optimized thin layer consisting of matrix and nitrocellulose has been developed. Piezoelectric microdispensing enabled sample depositions in a high-density array format of 2000 sample depositions on a conventionally sized target plate (45 x 47 mm). The sample depositions were made reproducibly in a fully automated mode by using an in-house developed computer-controlled piezoelectric flow-through microdispenser. Additionally, the piezoelectric technique facilitated significant analyte enrichment that increased the detection sensitivity. The MS signal was obtained rapidly, generally within ten laser pulses. An airbrush device was used to generate a fine spray of matrix and nitrocellulose dissolved in acetone. The acetone evaporated instantly when reaching the target plate leaving the entire surface with a thin and uniform matrix/nitrocellulose coating consisting of very small crystals of matrix embedded in the nitrocellulose. These crystals acted as a seed-layer on subsequent analyte depositions, rendering homogeneous sample spots when using alpha-cyano-4-hydroxycinnamic acid (CHCA) as matrix. The relative standard deviation of the signal intensity between spots was (20-30)% (n = 30). The detection sensitivity was improved by restricting the sample spot diameter to 300 microm. The spot size was affected by the deposition rate and the evaporation rate of the dispensed sample volume. Mass spectra of a 25-amol peptide mixture deposition were successfully recorded.     

Controlling matrix suppression for matrix‐assisted laser desorption/ionization analysis of small molecules

The need for high‐throughput methodologies providing both qualitative and quantitative information has grown substantially in the pharmaceutical laboratory in recent years. Currently, tandem mass spectrometry (MS/MS) using quadrupole technology offers analysis in the minutes time scale. The use of matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) offers the advantage of speed and automation and enables analysis in the seconds time scale with accurate mass capabilities that are not typically found in quadrupole MS/MS. However, one of the limitations of MALDI for the analysis of small molecules is the abundance of interfering matrix peaks in the low molecular weight region of the mass spectrum. Described herein is an evaluation of a pre‐prepared MALDI target plate that has been coated with a thin layer of α‐cyano‐4‐hydroxycinnamic acid (CHCA) and nitrocellulose. This modified plate has been shown to suppress or eliminate CHCA matrix signals without any significant loss of analyte sensitivity when compared with analysis of the same sample using an unmodified target plate. Copyright © 2004 John Wiley & Sons, Ltd.     

Investigations of matrix-assisted laser desorption/ionization sample preparation by time-of-flight secondary ion mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) analyses are compared to gain insight into some of the details of sample preparation for MALDI analysis of synthetic polymers. ToF-SIMS imaging of MALDI samples shows segregation of the cationization agent from the matrix crystals. The amount of observed segregation can be controlled by the sample preparation technique. Electrospray sample deposition minimizes segregation. Comparing ToF-SIMS and MALDI mass spectra from the same samples confirms that ToF-SIMS is significantly more surface sensitive than MALDI. This comparison shows that segregation of the oligomers of a polymer sample can occur during MALDI sample preparation. Our data indicate that MALDI is not as sensitive to those species dominating the sample surface as to species better incorporated into the matrix crystals. Finally, we show that matrix-enhanced SIMS can be an effective tool to analyze synthetic polymers, although the sample preparation conditions may be different than those optimized for MALDI.     

Simple fabrication of a structured matrix-assisted laser desorption/ionization target coating for increased sensitivity in mass spectrometric analysis of membrane proteins

A new prestructured target plate for matrix-assisted laser desorption/ionization (MALDI) was developed specifically for hydrophobic integral membrane proteins. This sample support contains predefined concentrating sample spots with a focusing effect on droplets with a high content of hexafluoroisopropanol (HFIP). This fluorinated organic solvent is advantageous for solubilizing hydrophobic proteins that are not soluble in water or the organic solvents normally used in sample preparation protocols for MALDI-MS. The prestructured plate was constructed by coating a regular steel plate with a thin layer of a silicone polymer, leaving sample spots of bare steel. Fabrication of the concentrating silicone structure was fast and very straightforward, without expensive or complicated equipment. Removing the layer, and thus regenerating the steel plate, was done by a simple washing procedure. The application and cleaning procedure are not constrained by a particular design of sample support or to any specific brand of mass spectrometer. When using the prestructured MALDI plate with HFIP as the sample solvent for 17 pmol of a cyanogen bromide digest of the highly hydrophobic membrane protein bacteriorhodopsin, an improved focusing effect and an increase of more than five-fold in average sensitivity were observed, compared with a regular steel target. Experimental results show a two-fold increase in average sensitivity when the new prestructured target plate was used, compared with a commercially available concentrating support.     

High‐resolution MALDI‐TOF MS study on analysis of low‐molecular‐weight products from photo‐oxidation of poly(3‐hexylthiophene)

High‐resolution matrix‐assisted laser desorption/ionization (MALDI) time‐of‐flight mass spectrometry (TOF MS) was used for the analysis of the low‐molecular‐weight products from the photo‐oxidation of poly(3‐hexylthiophene) (P3HT) in solution and thin film. Eight new peak series were observed in the low‐mass range of the mass spectra of the products degraded in solution, and the formulas of the eight components were determined from the accurate mass. From SEC/MALDI‐TOF MS, two components were identified as the degraded products, and the other six components were derived from the fragmentation of the degraded products during the MALDI process. A mechanism for the formation of these components was proposed on the basis of the results of MALDI‐TOF MS. For the thin film degradation, a part of products in the solution degradation were observed, which supports that the oxidation of P3HT in solution and thin film proceeded in the same mechanism. This study shows that high‐resolution MALDI‐TOF MS is effective for the analysis of the low‐molecular‐weight products from P3HT photo‐oxidation and expected to be feasible for the degradation analyses of other polymers. Copyright © 2015 John Wiley & Sons, Ltd.     

Plan-view preparation of TEM specimens from thin films using adhesive tape

A simple plan-view sample preparation technique for transmission electron microscopy (TEM) specimens is proposed for thin films by tearing-off the film with adhesive tape. The demand for very thin samples is highest for nanostructured materials where the structure of 2-5 nm sized features (grains) needs to be resolved; therefore, overlapping of nanometer-sized features should be avoided. The method provides thin areas at the fracture edges of plan-view specimens with thickness in the range of the grain size in the film allowing for artifact free high-resolution TEM imaging. Nanostructured materials typically fracture between the grains providing areas with the thickness of the grain size. Besides the swiftness of the method, the samples are free of surface amorphization artifacts, which can occur in ion beam milling up to 1 nm depth even at low energy ion bombardment. The thin film tear-off technique is demonstrated on a CuMn alloy thin film with grain size of 2 nm.     

Electrophoretic deposition of polyacrylic acid and composite films containing nanotubes and oxide particles

Electrophoretic deposition (EPD) method has been developed for the deposition of thin films of polyacrylic acid (PAA). This method allowed the formation of uniform films of controlled thickness on conductive substrates. It was shown that PAA can be used as a common dispersing agent suitable for charging and EPD of various materials, such as multiwalled carbon nanotubes, halloysite nanotubes, MnO(2), NiO, TiO(2) and SiO(2). The feasibility of EPD of composite films containing the nanotubes and oxide particles in a PAA matrix has been demonstrated. The kinetics of deposition and deposition mechanisms were investigated and discussed. The films were studied by thermogravimetric analysis, differential thermal analysis, X-ray diffraction and scanning electron microscopy. The results indicated that film thickness and composition can be varied. Obtained results pave the way for the fabrication of PAA and composite films for biomedical, electrochemical and other applications.     

Highly ordered polymer films of amphiphilic, regioregular polythiophene derivatives

The fabrication and characterization of highly ordered thin films made from amphiphilic, regioregular polythiophene derivatives are described. Films of poly(3-(11-(2-tetrahydropyranyloxy)undecyl)thiophene (PTHPUDT) were prepared by the Langmuir-Blodgett technique. The amphiphilic nature of the polymer affords layer-by-layer deposition and the formation of multilayer films of head-to-head and tail-to-tail Y-type structure. X-ray diffraction studies indicate bilayer separations of approximately 30 A. Anisotropic optical absorption in the plane of the film indicates that the thiophene backbones are preferentially oriented along the dipping direction. Further, polarized light microscopy studies indicate that these films are highly birefringent and that the optical retardation is uniform over the entire film. Ellipsometry studies confirm the sizable magnitude of the birefringence. Optical second-harmonic generation studies of multilayer films provide information regarding both the thiophene orientation within the film and the anisotropic distribution of chromophores in the surface plane. Taken together, these data offer strong evidence of highly ordered films in which the hydrophobic polythiophene chains lie parallel to the substrate surface with their alkyl chains oriented normal to the surface, as dictated by the hydrophilic nature of the alkyl chain's terminal tetrahydropyran functional group. As such, these films offer the potential for elucidating the connection between polymer morphology and physical property in materials that are otherwise subject to a sufficiently complex distribution of morphologies that such a correspondence is precluded.