In-Membrane Enrichment and Peptic Digestion to Facilitate Analysis of Monoclonal Antibody Glycosylation.

The number of therapeutic monoclonal antibodies (mAbs) is growing rapidly due to their widespread use for treating various diseases and health conditions. Assessing the glycosylation profile of mAbs during production is essential to ensuring their safety and efficacy. This research aims to rapidly isolate and digest mAbs for liquid chromatography-tandem mass spectrometry (LC-MS/MS) identification of glycans and monitoring of glycosylation patterns, potentially during manufacturing. Immobilization of an Fc region-specific ligand, oFc20, in a porous membrane enables the enrichment of mAbs from cell culture supernatant and efficient elution with an acidic solution. Subsequent digestion of the mAb eluate occurred in a pepsin-modified membrane within 5 min. The procedure does not require alkylation and desalting, greatly shortening the sample preparation time. Subsequent LC-MS/MS analysis identified 11 major mAb N-glycan proteoforms and assessed the relative peak areas of the glycosylated peptides. This approach is suitable for the glycosylation profiling of various human IgG mAbs, including biosimilars and different IgG subclasses. The total time required for this workflow is less than 2 h, whereas the conventional enzymatic release and labeling of glycans can take much longer. Thus, the integrated membranes are suitable for facilitating the analysis of mAb glycosylation patterns.

Addressing Challenges in Ion-Selectivity Characterization in Nanopores.

Ion selectivity is the basis for designing smart nanopore/channel-based devices, e.g., ion separators and biosensors. Quantitative characterization of ion selectivities in nanopores often employs the Nernst or Goldman-Hodgkin-Katz (GHK) equation to interpret transmembrane potentials. However, the direction of the measured transmembrane potential drop is not specified in these equations, and selectivity values calculated using absolute values of transmembrane potentials do not directly reveal the ion for which the membrane is selective. Moreover, researchers arbitrarily choose whether to use the Nernst or GHK equation and overlook the significant differences between them, leading to ineffective quantitative comparisons between studies. This work addresses these challenges through (a) specifying the transmembrane potential (sign) and salt concentrations in terms of working and reference electrodes and the solutions in which they reside when using the Nernst and GHK equations, (b) reporting of both Nernst-selectivity and GHK-selectivity along with solution compositions and transmembrane potentials when comparing different nanopores/channels, and (c) performing simulations to define an ideal selectivity for nanochannels. Experimental and modeling studies provide significant insight into these fundamental equations and guidelines for the development of nanopore/channel-based devices.

Analysis of Protein Glycosylation after Rapid Digestion Using Protease-Containing Membranes in Spin Columns.

Glycosylation is an important protein post-translational modification that plays a pivotal role in the bioactivity of therapeutic proteins and in the infectivity of viral proteins. Liquid chromatography with tandem mass spectrometry readily identifies protein glycans with site specificity. However, the overnight incubation used in conventional in-solution proteolysis leads to high turnaround times for glycosylation analysis, particularly when sequential in-solution digestions are needed for site-specific glycan identification. Using bovine fetuin as a model glycoprotein, this work first shows that in-membrane digestion in ∼3 min yields similar glycan identification and quantitation when compared to overnight in-solution digestion. Protease-containing membranes in a spin column enable digestion of therapeutic proteins (trastuzumab and erythropoietin) and a viral protein (SARS-CoV-2 receptor binding domain) in ∼30 s. Glycan identification is similar after in-solution and in-membrane digestion, and limited in-membrane digestion enhances the identification of high-mannose glycans in trastuzumab. Finally, stacked membranes containing trypsin and chymotrypsin allow fast sequential proteolytic digestion to site-specifically identify the glycans of SARS-CoV-2 receptor binding domain. One can easily assemble the protease-containing membranes in commercial spin columns, and spinning multiple columns simultaneously will facilitate parallel analyses.

Rapid Quantitation of Various Therapeutic Monoclonal Antibodies Using Membranes with Fc-Specific Ligands.

Therapeutic monoclonal antibodies (mAbs) provide effective treatments for many diseases, including cancer, autoimmune disorders, and, lately, COVID-19. Monitoring the concentrations of mAbs is important during their production and subsequent processing. This work demonstrates a 5 min quantitation of most human immunoglobulin G (IgG) antibodies through capture of mAbs in membranes modified with ligands that bind to the fragment crystallizable (Fc) region. This enables binding and quantitation of most IgG mAbs. Layer-by-layer (LBL) adsorption of carboxylic acid-rich polyelectrolytes in glass-fiber membranes in 96-well plates allows functionalization of the membranes with Protein A or a peptide, oxidized Fc20 (oFc20), with high affinity for the Fc region of human IgG. mAb capture occurs in <1 min during the flow of solutions through modified membranes, and subsequent binding of a fluorophore-labeled secondary antibody enables quantitation of the captured mAbs using fluorescence. The intra- and inter-plate coefficients of variations (CV) are <10 and 15%, respectively, satisfying the acceptance criteria for many assays. The limit of detection (LOD) of 15 ng/mL is on the high end of commercial enzyme-linked immunosorbent assays (ELISAs) but certainly low enough for monitoring of manufacturing solutions. Importantly, the membrane-based method requires <5 minutes, whereas ELISAs typically take at least 90 min. Membranes functionalized with oFc20 show greater mAb binding and lower LODs than membranes with Protein A. Thus, the membrane-based 96-well-plate assay, which is effective in diluted fermentation broths and in mixtures with cell lysates, is suitable for near-real-time monitoring of the general class of human IgG mAbs during their production.

Online protein digestion in membranes between capillary electrophoresis and mass spectrometry.

This research employs pepsin-containing membranes to digest proteins online after a capillary electrophoresis (CE) separation and prior to tandem mass spectrometry. Proteolysis after the separation allows the peptides from a given protein to enter the mass spectrometer in a single plug. Thus, migration time can serve as an additional criterion for confirming the identification of a peptide. The membrane resides in a sheath-flow electrospray ionization (ESI) source to enable digestion immediately before spray into the mass spectrometer, thus limiting separation of the digested peptides. Using the same membrane, digestion occurred reproducibly during 20 consecutive CE analyses performed over a 10 h period. Additionally, after separating a mixture of six unreduced proteins with CE, online digestion facilitated protein identification with at least 2 identifiable peptides for all the proteins. Sequence coverages were >75% for myoglobin and carbonic anhydrase II but much lower for proteins containing disulfide bonds. Development of methods for efficient separation of reduced proteins or identification of cross-linked peptides should enhance sequence coverages for proteins with disulfide bonds. Migration times for the peptides identified from a specific protein differed by <∼30 s, which allows for rejection of some spurious peptide identifications.

Nanopores: synergy from DNA sequencing to industrial filtration - small holes with big impact.

Nanopores in thin membranes play important roles in science and industry. Single nanopores have provided a step-change in portable DNA sequencing and understanding nanoscale transport while multipore membranes facilitate food processing and purification of water and medicine. Despite the unifying use of nanopores, the fields of single nanopores and multipore membranes differ - to varying degrees - in terms of materials, fabrication, analysis, and applications. Such a partial disconnect hinders scientific progress as important challenges are best resolved together. This Viewpoint suggests how synergistic crosstalk between the two fields can provide considerable mutual benefits in fundamental understanding and the development of advanced membranes. We first describe the main differences including the atomistic definition of single pores compared to the less defined conduits in multipore membranes. We then outline steps to improve communication between the two fields such as harmonizing measurements and modelling of transport and selectivity. The resulting insight is expected to improve the rational design of porous membranes. The Viewpoint concludes with an outlook of other developments that can be best achieved by collaboration across the two fields to advance the understanding of transport in nanopores and create next-generation porous membranes tailored for sensing, filtration, and other applications.

Ion Separations Based on Spontaneously Arising Streaming Potentials in Rotating Isoporous Membranes.

Highly selective ion separations are vital for producing pure salts, and membrane-based separations are promising alternatives to conventional ion-separation techniques. Our previous work demonstrated that simple pressure-driven flow through negatively charged isoporous membranes can separate Li+ and K+ with selectivities as high as 70 in dilute solutions. The separation mechanism relies on spontaneously arising streaming potentials that induce electromigration, which opposes advection and separates cations based on differences in their electrophoretic mobilities. Although the separation technique is simple, this work shows that high selectivities are possible only with careful consideration of experimental conditions including transmembrane pressure, solution ionic strength, the K+/Li+ ratio in the feed, and the extent of concentration polarization. Separations conducted with a rotating membrane show Li+/K+ selectivities as high as 150 with a 1000 rpm membrane rotation rate, but the selectivity decreases to 1.3 at 95 rpm. These results demonstrate the benefits and necessity of quantitative control of concentration polarization in highly selective separations. Increases in solution ionic strength or the K+/Li+ feed ratio can also decrease selectivities more than an order of magnitude.

Quantitation of Trastuzumab and an Antibody to SARS-CoV-2 in Minutes Using Affinity Membranes in 96-Well Plates.

Quantitation of therapeutic monoclonal antibodies (mAbs) in human serum could ensure that patients have adequate levels of mAbs for effective treatment. This research describes the use of affinity, glass-fiber membranes in a 96-well-plate format for rapid (<5 min) quantitation of the therapeutic mAb trastuzumab and a mAb against the SARS-CoV-2 spike protein. Adsorption of a poly(acrylic acid)-containing film in membrane pores and activation of the -COOH groups in the film enable covalent-linking of affinity peptides or proteins to the membrane. Passage of mAb-containing serum through the affinity membrane results in mAb capture within 1 min. Subsequent rinsing, binding of a secondary antibody conjugated to a fluorophore, and a second rinse yield mAb-concentration-dependent fluorescence intensities in the wells. Calibration curves established from analyses on different days have low variability and allow determination of mAb levels in separately prepared samples with an average error <10%, although errors in single-replicate measurements may reach 40%. The assays can occur in diluted serum with physiologically relevant mAb concentrations, as well as in undiluted serum. Thus, the combination of 96-well plates containing affinity membranes, a microplate reader, and a simple vacuum manifold affords convenient mAb quantitation in <5 min.

Electroblotting through Enzymatic Membranes to Enhance Molecular Tissue Imaging.

MALDI-TOF mass spectrometry imaging (MSI) is a powerful tool for studying biomolecule localization in tissue. Protein distributions in tissue provide important histological information; however, large proteins exhibit a high limit of detection in MALDI-MS when compared to their corresponding smaller proteolytic peptides. As a result, several techniques have emerged to digest proteins into more detectable peptides for imaging. Digestion is typically accomplished through trypsin deposition on the tissue, but this technique increases the complexity of the tissue microenvironment, which can limit the number of detectable species. This proof-of-principle study explores tryptic tissue digestion during electroblotting through a trypsin-containing membrane. This approach actively extracts and enzymatically digests proteins from mouse brain tissue sections while simultaneously reducing the complexity of the tissue microenvironment (compared to trypsin deposition on the surface) to obtain an increased number of detectable peptide fragments. The method does not greatly compromise spatial location or require expensive devices to uniformly deposit trypsin on tissue. Using electrodigestion through membranes, we detected and tentatively identified several tryptic peptides that were not observed after on-tissue digestion. Moreover, the use of pepsin rather than trypsin in digestion membranes allows extraction and digestion at low pH to detect peptides from a complementary subset of tissue proteins. Future studies will aim to further improve the method, including changing the substrate membrane to increase spatial resolution and the number of detected peptides.

Determination of the Serum Concentrations of the Monoclonal Antibodies Bevacizumab, Rituximab, and Panitumumab Using Porous Membranes Containing Immobilized Peptide Mimotopes.

Effective monoclonal antibody (mAb) therapies require a threshold mAb concentration in patient serum. Moreover, the serum concentration of the mAb Bevacizumab should reside in a specific range to avoid side effects. Methods for conveniently determining the levels of mAbs in patient sera could allow for personalized dosage schedules that lead to more successful treatments. This work utilizes microporous nylon membranes functionalized with antibody-binding peptides to capture Bevacizumab, Rituximab, or Panitumumab from diluted (25%) serum. Modification of the capture-peptide terminus is often crucial to creating the affinity necessary for effective binding. The high purity of eluted mAbs allows for their quantitation using native fluorescence, and membranes are effective in spin devices that can be used in any laboratory. The technique is effective over the therapeutic range of Bevacizumab concentrations. Future work aims at further modifications to develop rapid point-of-care devices and decrease detection limits.

Highly Rectifying Fluidic Diodes Based on Asymmetric Layer-by-Layer Nanofilms on Nanochannel Membranes.

Nanochannel-based fluidic diodes display ion selectivity and ion current rectification (ICR), which may prove to be important in energy-harvesting devices and biosensors. This paper reports asymmetric functionalization of the outer surface of a flexible nanochannel polymer membrane to create fluidic diodes that give ICR. Layer-by-layer (LbL) adsorption with cross-linking of only the underlying part of the polyelectrolyte nanofilm leads to a porosity step across the film. The combination of a high effective surface charge density and the porosity step in the film leads to a remarkable maximum ICR factor of ∼200 with a pH gradient across the film. Incorporation of pH-sensitive polyelectrolyte components enables the ICR factor to increase an order of magnitude on going from pH 8 to pH 3. Moreover, the coated membrane shows excellent anion selectivity. Thus, LbL adsorption with partial cross-linking provides a simple method for creating coated nanochannel membranes that serve as pH-responsive ionic diodes for potential chemical/biosensors.

Membrane-Based Affinity Purification to Identify Target Proteins of a Small-Molecule Drug.

Identifying the target proteins of small-molecule drug candidates is important for determining their molecular mechanisms of action. Porous membranes derivatized with such small molecules may provide an attractive target-identification platform due to a high protein-capture efficiency during flow through membrane pores. This work employs carbonic anhydrase II (CAII) binding to immobilized 4-(2-aminoethyl)benzenesulfonamide (AEBSA) to examine the efficiency and selectivity of affinity capture in modified membranes. Selective elution of captured protein, tryptic digestion, tandem mass spectrometry analysis, and label-free quantification (LFQ) identify CAII as the dominant AEBSA target in diluted serum or cell lysate. CAII identification relies on determining the ratio of protein LFQ intensities in sample and control experiments, where free AEBSA added to the control loading solution limits CAII capture. Global proteomics shows that the spiked CAII is the only protein with a log2 ratio consistently >2, and the detection limit for CAII identification is 0.004 wt % of the total protein in 1:4 diluted human serum or 0.024 wt % of the total protein from breast cancer cell lysates. The same approach also identifies native CAII in human kidney cell lysate as an AEBSA target. Comparison of affinity capture using membranes, Affi-Gel 10 resin or M-270 Dynabeads derivatized with AEBSA suggests that only membranes allow identification of low-abundance CAII as a target.

Flow through negatively charged, nanoporous membranes separates Li+ and K+ due to induced electromigration.

Flow through negatively charged nanopores separates Li+ and K+ with selectivities of up to 70 and Li+ passages from 20% to above 100%. Remarkably, both the Li+/K+ selectivity and Li+ passage initially increase with flow rate, breaking the permeability/selectivity trade-off. Modelling demonstrates that flow through the membranes creates electric fields that retard transport of cations. Selectivity increases with flow rate because the K+ electromigration velocity exceeds its convective velocity, but for Li+ electromigration is weaker than convection. Modelling also shows the importance of controlling concentration polarization. With further work, related separations might provide highly pure Li salts for battery manufacturing.

Oil droplet behavior on model nanofiltration membrane surfaces under conditions of hydrodynamic shear and salinity.

HYPOTHESES: Oil droplet stability and electrical charge, and membrane's affinity for oil govern droplet attachment to a membrane surface. Moderate droplet-surface affinity encourages surface coalescence and removal of droplets to help maintain the membrane relatively oil-free. EXPERIMENTS: Droplet attachment onto model nanofiltration membranes was studied, in situ and in real time, using the Direct Observation Through the Membrane method. Optically transparent nanofiltration membranes were designed by forming polyelectrolyte multilayer films, with either positively or negatively charged surfaces, on Anopore ultrafilters. Crossflow across the membrane surface employed hexadecane-in-water emulsions stabilized by an anionic surfactant (sodium dodecylsulfate) in model sea water or aqueous solutions containing NaCl or MgSO4. FINDINGS: Moderate affinity between oil and the polyelectrolyte-coated surface promotes crossflow controlled coalescence to remove droplets larger than a critical size, ddropcrit, in the crossflow shear. The torque balance on a sessile oil droplet in a linear shear field overpredicted ddropcrit pointing to a need for more accurate estimates of lift and drag forces on a droplet. In the presence of divalent cations, lower electrostatic repulsion between droplets facilitated droplet-droplet adhesion and led to rapid coalescence that resulted in membrane fouling. The most significant fouling appeared in tests with positively charged and less oleophobic coatings.

A Limiting Case of Constant Counterion Electrochemical Potentials in the Membrane for Examining Ion Transfer at Ion-Exchange Membranes and Patches.

Ion passage through ion-exchange membranes is vital in electrodialysis desalination, batteries and fuel cells, and water splitting. Simplified models of ion transport through such membranes frequently assume complete exclusion of co-ions (ions with the same sign of charge as the fixed charge in the membrane) from the membrane. However, a second assumption of constant counterion electrochemical potentials across the membrane leads to simple analytical expressions for ion fluxes and transmembrane potentials. Moreover, linear corrections to account for a small membrane electrical resistance yield analytical expressions with a wider applicability. For bi-ionic potential measurements and current-induced concentration polarization at low salt concentrations, these analytical solutions match the fluxes and potentials obtained numerically without the limiting assumptions. This gives confidence in both the limiting assumptions (under appropriate conditions) and the numerical solutions. At low ion concentrations, the analytical solutions may enable rapid characterization of membrane coatings or boundary layers in solution, and such boundary layers are important in many applications of ion-exchange membranes. In fact, the assumption of complete co-ion exclusion is sometimes more limiting than the constraint of constant electrochemical potentials of counterions across the membrane. Remarkably, this limiting case readily yields the ion accumulation and depletion regions above "ion-exchange patches" that reside beneath a solution with an applied electric field. Such regions are important for sample preconcentration in microfluidic devices.

Modelling nanofiltration of electrolyte solutions.

This review critically examines current models for nanofiltration (NF) of electrolyte solutions. We start from linear irreversible thermodynamics, we derive a basic equation set for ion transfer in terms of gradients of ion electrochemical potentials and transmembrane volume flux. These equations are extended to the case of significant differences of thermodynamic forces across the membrane (continuous version of irreversible thermodynamics) and solved in quadratures for single salts and trace ions added to single salts in the case of macroscopically-homogeneous membranes. These solutions reduce to (quasi)analytical expressions in the popular Spiegler-Kedem approximation (composition-independent phenomenological coefficients), which we extend to the case of trace ions. This enables us to identify membrane properties (e.g. ion permeances, ion reflection coefficients, electrokinetic charge density) that control its performance in NF of multi-ion solutions. Further, we specify the phenomenological coefficients of irreversible thermodynamics in terms of ion partitioning, hindrance and diffusion coefficients for the model of straight cylindrical capillaries. The corresponding expressions enable assessment of the applicability of the popular nanopore model of NF. This model (based on the use of macroscopic approaches at nanoscale) leads to a number of trends that have never been observed experimentally. We also show that the use of the Born formula (frequently employed for the description of dielectric exclusion) hardly leads to meaningful values of solvent dielectric constant in membrane pores because this formula disregards the very solvent structure whose changes are supposed to bring about the reduction of dielectric permittivity in nanopores. We conclude that the effect should better be quantified in terms of ion excess solvation energies in the membrane phase. As an alternative to the nanopore description of NF, we review recent work on the development of an advanced engineering model for NF of multi-ion solutions in terms of a solution-diffusion-electromigration mechanism. This model (taking into account spontaneously arising transmembrane electric fields) captures several trends observed experimentally, and the use of trace ions can provide model parameters (ion permeances in the membrane) from experiment. We also consider a recent model (ultrathin barrier layers with deviations from local electroneutrality) that may reproduce observed feed-salt concentration dependences of membrane performance in terms of concentration-independent properties like excess ion solvation energies. Due to its complexity, practical modelling of nanofiltration will probably be performed with advanced engineering models for the foreseeable future. Although mechanistic studies are vital for understanding transport and developing membranes, future simulations in this area will likely need to depart from typical continuum models to provide physical insight. For enhancing the quality of modelling input, it is essential to improve the control of concentration polarization in membrane test cells.

High Selectivities among Monovalent Cations in Dialysis through Cation-Exchange Membranes Coated with Polyelectrolyte Multilayers.

Cation-exchange membranes allow preferential passage of cations over anions, but they show minimal selectivity among cations, which limits their use in ion separations. Recent studies show that modification of cation-exchange membranes with polyelectrolyte multilayers leads to exceptional monovalent/divalent cation electrodialysis selectivities, but no studies report high selectivity among monovalent ions. This work demonstrates that adsorption of protonated poly(allylamine) (PAH)/poly(4-styrenesulfonate) (PSS) multilayers on Nafion membranes leads to high K+/Li+ selectivities in Donnan dialysis, where K+ and Li+ ions in a source phase pass through the membrane and exchange with Na+ ions in a receiving phase. Addition of 0.01 M HNO3 to a source phase containing 0.01 M KNO3 and 0.01 M LiNO3 increases the K+/Li+ selectivity from 8 to ∼60 through (PAH/PSS)5PAH-coated Nafion membranes, primarily because of a ≥fivefold increase in K+ flux. These selectivities are much larger than the ratio of 1.9 for the aqueous diffusion coefficients of K+ and Li+, and uncoated Nafion membranes give a K+/Li+ selectivity <3. Bi-ionic transmembrane potential measurements at neutral pH confirm that the membrane is more permeable to K+ than Li+, but this selectivity is less than in Donnan dialysis with acidic solutions. In situ ellipsometry data indicate that PAH/PSS multilayers (assembled at pH 2.3, 7.5, or 9.3) swell at pH 2.0, and this swelling may open cation-exchange sites that preferentially bind K+ to enable highly selective transport. The coated membranes also exhibit modest selectivity for K+ over H+, suggesting selective transport based on preferential partitioning of K+ into the coatings. Selectivity declines when increasing the source-phase KNO3 concentration to 0.1 M, perhaps because the discriminating transport pathway saturates. Moreover, selectivities are lower in electrodialysis than in Donnan dialysis, presumably because electrodialysis engages other transport mechanisms, such as electroosmosis and strong electromigration.

Monoclonal Antibody Capture and Analysis Using Porous Membranes Containing Immobilized Peptide Mimotopes.

Rapid, convenient methods for monoclonal antibody (mAb) isolation are critical for determining the concentrations of therapeutic mAbs in human serum. This work uses porous nylon membranes modified with a HER2 peptide mimotope, KGSGSGSQLGPYELWELSH (KH19), for rapid affinity capture of Herceptin, a mAb used to treat breast cancer. Covalent linking of KH19 to poly(acrylic acid)-containing films in porous nylon leads to a Herceptin-binding capacity of 10 mg per mL of membrane and allows selective Herceptin capture from diluted (1:3) human serum in 5 min. Liquid chromatography-mass spectrometry demonstrates the high purity of eluted Herceptin. Moreover, the fluorescence intensity of the protein eluted from membranes increases linearly with the amount of Herceptin spiked in loading solutions containing diluted (1:3) human serum. These results demonstrate the promise of mimotope-modified membranes for Herceptin analysis that does not require secondary antibodies or derivatization with fluorescent labels. Thus, mimotope-containing membranes may form part of a simple benchtop analysis system for assessing the concentrations of therapeutic mAbs.

Enzyme-containing spin membranes for rapid digestion and characterization of single proteins.

Proteolytic digestion is an important step in characterizing protein sequences and post-translational modifications (PTMs) using mass spectrometry (MS). This study uses pepsin- or trypsin-containing spin membranes for rapid digestion of single proteins or simple protein mixtures prior to ultrahigh-resolution Orbitrap MS analysis. Centrifugation of 100 µL of pretreated protein solutions through the functionalized membranes requires less than 1 min and conveniently digests proteins into large peptides that aid in confirming specific protein sequence variations and PTMs. Peptic and tryptic peptides from spin digestion of apomyoglobin and four commercial monoclonal antibodies (mAbs) typically cover 100% of the protein sequences in direct infusion MS analysis. Increasing the spin rate leads to a higher fraction of large peptic peptides for apomyoglobin, and MS analysis of peptic and tryptic peptides reveals mAb PTMs such as N-terminal pyroglutamate formation, C-terminal lysine clipping and glycosylation. Relative to overnight in-solution digestion of mAbs, spin digestion yields higher sequence coverages. Spin-membrane digestion followed by infusion MS readily differentiates a mAb to the Ebola virus from a related antibody that differs by addition of a single amino acid.

Limited proteolysis in porous membrane reactors containing immobilized trypsin.

Proteolysis is often a critical step in protein characterization via mass spectrometry. Compared to complete digestion, limited proteolysis gives larger peptides, and the dominant cleavage sites may identify highly accessible, flexible protein regions. This paper explores controlled proteolysis in porous nylon membranes containing immobilized trypsin. Passage of protein solutions through ∼100 µm thick membranes provides reaction residence times as short as milliseconds to limit digestion. Additionally, variation of the membrane pore size and the protease-immobilization method (electrostatic adsorption or covalent anchoring to adsorbed polymer in membrane pores) affords control over the proteolysis rate. When digesting the highly labile protein ß-casein, large membrane pores (5.0 µm) and covalent enzyme anchoring to adsorbed polymer lead to particularly long tryptic peptides. With the more trypsin-resistant proteins cytochrome c and apomyoglobin, in-membrane proteolysis with short residence times, 1.2 µm membrane pores, and trypsin electrostatically immobilized to an adsorbed polyanion cleaves the proteins after lysine residues in flexible regions. For both cytochrome c and apomyoglobin, cleavages in an interhelix region yield two particularly large peptides that cover the entire protein sequence.