Separation Of Peptides Research Articles

Serum proteomic pattern in female stress urinary incontinence.

The pathophysiology of Stress Urinary Incontinence (SUI) is poorly understood. The aim of this study was to identify the serum proteomic profile in patients with SUI and to replicate findings from a preceding study in which a significant difference in the urinary proteome was identified. Serum samples were collected from 38patients (19 SUI; 19 matched, continent controls). Sample preparation included serum albumin depletion, in-solution enzymatic digestion of proteins applying a combination of Gluc-C and trypsin and peptide separation using nano High Performance Liquid Chromatography. Label-free quantitation of peptides and proteins was performed after triplicate measurements using quadrupole time-of-flight mass spectrometry. Peptide identification was achieved by searching the Human SwissProt Database using Mascot and X!Tandem. Main outcome measure was the relative abundance of each detected protein in serum. Of 7012 identified proteins, 33 proteins were induced (detected in SUI, not in controls) and five proteins were depleted (detected in controls, not in SUI). All depleted proteins play a role in immune/DNA damage response. Induced proteins are involved in inflammatory response, response to cellular stress, coagulation and cytoskeleton stability/ motility. Plasma serine protease inhibitor (SERPINA5) was found induced and previously also showed a higher abundance in urine samples of SUI patients. Data are available via ProteomeXchange with identifier PXD008553.

Strong cation exchange-reversed phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry platform with high peak capacity for deep bottom-up proteomics

Two-dimensional (2D) liquid chromatography (LC)-tandem mass spectrometry (MS/MS) are typically employed for deep bottom-up proteomics, and the state-of-the-art 2D-LC-MS/MS has approached over 8000 protein identifications (IDs) from mammalian cell lines or tissues in 1–3 days of mass spectrometer time. Capillary zone electrophoresis (CZE)-MS/MS has been suggested as an alternative to LC-MS/MS for bottom-up proteomics. CZE-MS/MS and LC-MS/MS are complementary in protein/peptide ID from complex proteome digests because CZE and LC are orthogonal for peptide separation. In addition, the migration time of peptides from CZE-MS can be predicted accurately, which is invaluable for evaluating the confidence of peptide ID from the database search and even guiding the database search. However, the number of protein IDs from complex proteomes using CZE-MS/MS is still much lower than the state of the art using 2D-LC-MS/MS. In this work, for the first time, we established a strong cation exchange (SCX)-reversed phase LC (RPLC)-CZE-MS/MS platform for deep bottom-up proteomics. The platform identified around 8200 protein groups and 65,000 unique peptides from a mouse brain proteome digest in 70 h. The data represents the largest bottom-up proteomics dataset using CZE-MS/MS and provides a valuable resource for further improving the tool for prediction of peptide migration time in CZE. The peak capacity of the orthogonal SCX-RPLC-CZE platform was estimated to be around 7000. SCX-RPLC-CZE-MS/MS produced comparable numbers of protein and peptide IDs with 2D-LC-MS/MS (8200 vs. 8900 protein groups, 65,000 vs. 70,000 unique peptides) from the mouse brain proteome digest using comparable instrument time. This is the first time that CZE-MS/MS showed its capability to approach comparable performance to the state-of-the-art 2D-LC-MS/MS for deep proteomic sequencing. SCX-RPLC-CZE-MS/MS and 2D-LC-MS/MS showed good complementarity in protein and peptide IDs and combining those two methods improved the number of protein group and unique peptide IDs by nearly 10% and over 40%, respectively, compared with 2D-LC-MS/MS alone.

Recent trends and analytical challenges in plant bioactive peptide separation, identification and validation.

Interest in research into bioactive peptides (BPs) is growing because of their health-promoting ability. Several bioactivities have been ascribed to peptides, including antioxidant, antihypertensive and antimicrobial properties. As they can be produced from precursor proteins, the investigation of BPs in foods is becoming increasingly popular. For the same reason, production of BPs from by-products has also emerged as a possible means of reducing waste and recovering value-added compounds suitable for functional food production and supplements. Milk, meat and fish are the most investigated sources of BPs, but vegetable-derived peptides are also of interest. Vegetables are commonly consumed, and agro-industrial wastes constitute a cheap, large and lower environmental impact source of proteins. The use of advanced analytical techniques for separation and identification of peptides would greatly benefit the discovery of new BPs. In this context, this review provides an overview of the most recent applications in BP investigations for vegetable food and by-products. The most important issues regarding peptide isolation and separation, by single or multiple chromatographic techniques, are discussed. Additionally, problems connected with peptide identification in plants and non-model plants are discussed regarding the particular case of BP identification. Finally, the issue of peptide validation to confirm sequence and bioactivity is presented. Graphical representation of the analytical workflow needed for investigation of bioactive peptides and applied to vegetables and vegetable wastes Graphical Abstract.

Design of peptide–dendrimer conjugates with tumor homing and antitumor effects

Development of drug delivery systems for cancer therapy is a crucial issue. Previously, some peptides were designed as tumor homing cell-penetrating peptides with antitumor activities. In this study, dual function dendrimers with tumor targeting activities and antitumor effects were designed using the tumor targeting CPP44 peptide for acute myelogenous leukemia (AML) and the antitumor p16INK4a peptide. Two types of peptide–dendrimer conjugates were synthesized. One was a CPP44-linked p16INK4a peptide-conjugated dendrimer (tandem linked dendrimer) and the other was a dendrimer conjugated with separate CPP44 and p16INK4a peptides (parallel linked dendrimer). In addition, a peptide cathepsin B substrate was linked to the antitumor p16INK4a peptide to release it from the carriers. These peptide–dendrimer conjugates produced more effective antitumor effects than a CPP44-linked p16INK4a peptide. The parallel linked dendrimer showed less association with AML cells than the tandem linked dendrimer, but had greater antitumor effects. This suggested that both cellular uptake and antitumor peptide cleavage affected the antitumor activities of dual functional peptide-conjugated dendrimers.

Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis.

Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.

Separation and Identification of Glutamine Peptides from Defatted Soybean Meal by Enzymatic Hydrolysis

Abstract: Glutamine peptides were obtained from defatted soybean meal by enzymatic hydrolysis using a combination of Protamex® and trypsinase. The results showed that the extent of hydrolysis and the concentration of Gln peptides in the hydrolysate were 22.02% and 6.05 mmol/L, respectively. The hydrolysates were fractionated by size-exclusion chromatography on a Sephadex G-15 into five major fractions (GelF1–GelF5). The peptide (GelF1) fraction with the highest glutamine peptide content (51.8%) was further evaluated to determine its molecular weight distribution. Most (92.37%) peptides were less than 1 000 Da. Glutamic acid and glutamine were the most abundant amino acids, accounting for up to 12.98% of the total amino acid content. In addition, the total amino acid content in GelF1 was higher than that in GelF2 and GelF3. Supported by National Key R&D Program of China (2016YFD0400203).

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.

Isolation and evaluation of two angiotensin-I-converting enzyme inhibitory peptides from fermented grains (Jiupei) used in Chinese Baijiu production.

In the present study, fermented grains (Jiupei), the raw material for Baijiu distillation, were used to isolate and identify low molecular weight peptides with angiotensin-I-converting enzyme (ACE) inhibitory activities. The methods of peptides extraction from Jiupei are described as follows: ultrasonication, centrifugation and filtration. Peptide purification was performed by ultrafiltration, adsorption on a macroporous resin, gel chromatography and reversed-phase high-performance liquid chromatography (RP-HPLC). HPLC with quadrupole-time-of-flight-mass spectrometry/mass spectrometry (HPLC-Q-TOF-MS/MS) was used to identify the peptides, and the ACE inhibitory activities of the peptides were measured. Finally, the optimum peptide extraction and separation parameters were determined to be a liquid/solid (ultrapure water/Jiupei powder) ratio of 15 mL g−1, extraction temperature of 57 °C and ultrasonication time of 33 min. XAD-16 resin was used for the removal of sugars and salts. Under these conditions, the total yield of peptides extracted was 57.682 mg/1 g Jiupei. The peptides identified were Val-Asn-Pro and Tyr-Gly-Asp. Val-Asn-Pro exhibited some ACE inhibitory activity (IC50 = 38.02 μM), while Tyr-Gly-Asp showed higher ACE inhibitory activity (IC50 = 5.21 μM). These results provide an important foundation for the study of peptides in Jiupei and show a reference for the trace of peptides in Baijiu production.

Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of

Multidimensional peptide separations can greatly increase the depth of coverage in proteome profiling. However, a major challenge for multidimensional separations is the requirement of large biological samples, often containing milligram amounts of protein. We have developed nanowell-mediated two-dimensional (2D) reversed-phase nanoflow liquid chromatography (LC) separations for in-depth proteome profiling of low-nanogram samples. Peptides are first separated using high-pH LC and the effluent is concatenated into 4 or 12 nanowells. The contents of each nanowell are reconstituted in LC buffer and collected for subsequent separation and analysis by low-pH nanoLC-MS/MS. The nanowell platform minimizes peptide losses to surfaces in offline 2D LC fractionation, enabling >5800 proteins to be confidently identified from just 50 ng of HeLa digest. Furthermore, in combination with a recently developed nanowell-based sample preparation workflow, we demonstrated deep proteome profiling of >6000 protein groups from small populations of cells, including ∼650 HeLa cells and 10 single human pancreatic islet thin sections (∼1000 cells) from a pre-symptomatic type 1 diabetic donor.

Separation and identification of peptides from dry-cured Jinhua ham

ABSTRACTA long ripening period is essential for the production of dry-cured ham. This ripening process results in the generation of a large number of small peptides that are responsible for the ham’s flavour. In this study, peptides extracted from Jinhua ham were separated and purified using a tangential flow filter and Sephadex G-25 gel filtration chromatography and identified using liquid chromatography-tandem mass spectrometry. Sixty-three peptides were identified within the range between 227.1 and 1540.8 Da, including 10 dipeptides, 14 tripeptides, 12 tetrapeptides, eight pentapeptides, eight hexapeptides, four heptapeptides, one octopeptide, three nonapeptides, one decapeptide, one dodecapeptide, and one tridecapeptide. The most abundant peptides (and their relative peak areas) were Leu-Pro-Lys (10.49%), Ser-Gly-Leu (8.72%), Ala-Ala-Pro (7.36%), Val-Glu (5.62%), Pro-Leu (3.83%), Ser-Gly-Val (3.77%), Ala-His (3.40%), Ala-Arg (3.37%), and Leu-His-Ala (3.03%). The peptide sequence results provide novel information that contributes to a better understanding of proteolysis and fundamental peptide characterizations.Abbreviations: L, Leu; P, Pro; K, Lys; S, Ser; G, Gly; L, Lys; A, Ala; V, Val; E, Glu; H, His; R, Arg; T, Thr; C, Cys; I, Ile; N, Asn; D, Asp; Q, Gln; Y, Tyr; M, Met; W, Trp; F, Phe; DPP, dipeptidyl peptidase; TPP, tripeptidyl peptidase; LAP, Leu aminopeptidase; AAP, Ala aminopeptidase; RAP, Arg aminopeptidase; TFF, tangential flow filter

The influence of pH on retention and migration of peptides in systems with octadecyl silica-based adsorbent by high-performance thin-layer chromatography and pressurized planar electrochromatography techniques

In our paper we investigate the influence of pH of the mobile phase buffer, on retention of peptides in both: normal phase (NP) and reversed phase (RP) high-performance thin-layer chromatography systems (HPTLC), using C18 silica-based adsorbent. We also compare the influence of pH on retention and/or migration distance of peptides in separation systems of HPTLC and PPEC (pressurized planar electrochromatography) techniques. Our results show, that the change of pH of the mobile phase buffer can be used for two-dimensional HPTLC separation of peptides, but much stronger change of separation selectivity can be obtained by overall inversion of separation system type (NP/RP), as we have described before (Gwarda et al., 2016). In PPEC influence of the mobile phase pH on selectivity of peptide separation is very clear and strictly different than that in HPTLC (including overall inversion of direction of solutes migration), what results from the significant share of electrophoretic effect in overall mechanism of separation. Migration of peptides in two opposite directions results in better selectivity of separation by PPEC. In separation systems of both HPTLC and PPEC techniques, the change of pH clearly affects the efficiency of the separation system, so it can be used for optimization of separation conditions. Our results also show, that some modifications of PPEC equipment and materials could be useful for application of this technique in the field of peptide analysis.

Peptide retention time prediction in hydrophilic interaction liquid chromatography. Comparison of separation selectivity between bare silica and bonded stationary phases

Peptide separation selectivity of four different HILIC sorbents was compared through the development of sequence-specific retention prediction algorithms for the datasets of 36–40 thousands peptides each. Hydrophilicity of these sorbents at pH 4.5 (peptide retention under acetonitrile:water gradients) increases in the following order: Luna HILIC < XBridge Amide < Atlantis Silica ∼ Luna HILIC Silica. Bare silica phases are characterized by higher retention coefficients for basic residues (Arg, Lys, His), while interactions with neutral HILIC phases is driven by interaction with the charged residues (Asp, Glu, Arg, Lys, His). Such difference is caused by electrostatic repulsion of negatively charged side chains of Asp and Glu from silanol groups on bare silica sorbents. The sequence-specific features characteristic for both bonded and bare-silica supports were established. Variation of retention coefficients at N- and C-termini showed a peptide orientation effect on silica matrices. The negatively charged surface of silica attracts positively charged groups, thus increasing interaction of N-terminal residues. The effect of peptide helicity is also different between two types of sorbents. The contribution of amphipathic helicity was found to be higher for more hydrophilic silica matrices, causing a reduced predictive accuracy of the models: all four Sequence-Specific Retention Calculator HILIC models had R2-values in 0.973–0.98 range. Development of accurate prediction models provides a solid support for retention prediction filtering of false positive identifications in high-throughput proteomics analyses, guided development of 2D LCMS procedures ((HILIC-RP)). Our analysis also shows that all phases possess a high degree of orthogonality to RPLC (formic acid) with Luna HILIC being the best choice in this regard.

Separation and identification of bromelain-generated antibacterial peptides from Actinopyga lecanora.

Actinopyga lecanora, as a rich protein source was hydrolysed to generate antibacterial bioactive peptides using different proteolytic enzymes. Bromelain hydrolysate, after 1h hydrolysis, exhibited the highestantibacterial activities against Pseudomonas aeruginosa, Pseudomonas sp., Escherichia coli and Staphylococcus aureus. Two dimensional fractionation strategies, using a semi-preparative RP-HPLC and an isoelectric-focusing electrophoresis, were applied for peptide profiling. Furthermore, UPLC-QTOF-MS was used for peptides identification; 12 peptide sequences were successfully identified. The antibacterial activity of purified peptides from A. lecanora on P. aeruginosa, Pseudomonas sp., E. coli and S. aureus was investigated. These identified peptides exhibited growth inhibition against P. aeruginosa, Pseudomonas sp., E. coli and S. aureus with values ranging from 18.80 to 75.30%. These results revealed that the A. lecanora would be used as an economical protein source for the production of high value antibacterial bioactive peptides.

Efficient Therapeutic Protein Expression Using Retroviral Replicating Vector with 2A Peptide in Cancer Models.

Toca 511, a retroviral replicating vector (RRV), uses an internal ribosomal entry site (IRES) to express an optimized yeast cytosine deaminase (yCD2), which converts 5-fluorocytosine to 5-fluorouracil. This configuration is genetically stable in both preclinical mouse models and human clinical trials. However, the use of IRES (∼600 bp) restricts choices of therapeutic transgenes due to limits in RRV genome size. This study replaced IRES with 2A peptides derived from picornaviruses with or without a GSG linker. The data show that GSG-linked 2A (g2A) peptide resulted in higher polyprotein separation efficiency than non-GSG linked 2A peptide. The study also shows that RRV can tolerate insertion of two separate 2A peptides to allow expression of two transgenes without compromising the assembly and function of the virus in addition to insertion of a single 2A peptide to confirm genetic stability with yCD2, green fluorescent protein, and HSV-1 thymidine kinase. In a parallel comparison of the RRV-IRES-yCD2 and RRV-g2A-yCD2 configurations, the study shows the yCD2 protein expressed from RRV-g2A-yCD2 has higher activity, resulting in a higher survival benefit in an intracranial tumor mouse model. These data enable a wider range of potential product candidates that could be developed using the RRV platform.

Utilization of blood by-products: An in silico and experimental combined study for BSA usage

In order to exploit industrial discards, protein enzymatic hydrolysis is a currently popular methodology for obtaining bioactive peptides. However, once released, most promising peptides have to be selected from the mixture. In this work, the suitability of pepsin (EC 3.4.23.1) to hydrolyse serum albumin in order to obtain bioactive peptides was assessed. Then, a suitable process to obtain best separation of bioactive peptides was evaluated, using polyethersulfone membranes at different pH values. Serum albumin was easily hydrolysed by pepsin, reaching a DH value of the 65.64 ± 1.57% of the maximum possible. A 23.25% of the identified peptides possessed high bioactivity scores (greater than 0.5), and one of them had reported bioactivity (LLL). Charge mechanisms always predominated over the sieve effect, and best transmission was accomplished at pH values close to the peptides isoelectric points. Basic and neutral peptides with the highest scores were always the most transmitted. Membrane material had greater influence than NMWCO in determining peptide transmission. In order to obtain purified fractions rich in peptides with high bioactivity scores from serum albumin, polyethersulfone membranes (applicable to industrial scale) of 5 kDa MWCO should be used at basic pH values after pepsin digestion.

Predictive Liquid Chromatography of Peptides Based on Hydrophilic Interactions for Mass Spectrometry-Based Proteomics

High-performance liquid chromatography (HPLC) is widely used for separation of complex peptide mixtures before mass spectrometry-based proteome analysis. In this analysis, reversed phase HPLC (RPHPLC) using non-polar stationary phases such as surface-modified silica containing alkyl groups (e.g., C18) is typically employed. Because of the high heterogeneity of proteomic samples, multidimensional separation approaches gained increasing attention recently to tackle this complexity and extremely high range of concentrations. In two-dimensional liquid chromatography, hydrophilic interaction chromatography (HILIC) is often a method of choice for combination with RP-HPLC because it uses reversed-phase type eluents and allows efficient separation of polar peptides. Due to the high degree of orthogonality in this two-dimensional separation space, it is tempting to develop approaches for predicting peptide retention times for HILIC-based separations similar to the ones for RP-HPLC. Recent successful efforts in this area were focused on developing retention coefficient (RC)-based approaches. Herein, we explored the feasibility of using a statistical thermodynamic model for prediction of peptide retention times in HILIC separations and determined the phenomenological parameters of the model for a bare silica column. The performance of the developed model was tested using HPLC-MS analysis of a set of synthetic peptides, as well as a tryptic peptide mixture.

Differential Ion Mobility Separations in the Low-Pressure Regime.

Ion mobility spectrometry (IMS) in conjunction with mass spectrometry (MS) has emerged as a powerful platform for biological and environmental analyses. An inherent advantage of differential or field asymmetric waveform IMS (FAIMS) based on the derivative of mobility vs electric field over linear IMS based on absolute mobility is much greater orthogonality to MS. Effective coupling of linear IMS to MS and diverse IMS/MS arrangements and modalities impossible at ambient buffer gas pressure were enabled at much reduced pressures. In contrast, FAIMS devices operate at or near atmospheric pressure, which complicated integration with MS. Here, we show FAIMS at ∼15-30 Torr using a planar-gap stage within the MS instrument envelope. Fields up to ∼300 Td permitted by the Paschen law at these pressures greatly raise the separation speed, providing fair resolution in ∼10 ms and FAIMS scans in under 5 s. Rapid separation and efficient ion collection at low pressure minimize losses in the FAIMS step. Separations for key analyte classes and their dependences on electric field mirror those at ambient pressure. The potential for proteomics is demonstrated by separations of isomeric peptides with variant localization of post-translational modifications.

Detailed Evidence for an Unparalleled Interaction Mode between Calmodulin and Orai Proteins.

Calmodulin (CaM) binds most of its targets by wrapping around an amphipathic α-helix. The N-terminus of Orai proteins contains a conserved CaM-binding segment but the binding mechanism has been only partially characterized. Here, microscale thermophoresis (MST), surface plasmon resonance (SPR), and atomic force microscopy (AFM) were employed to study the binding equilibria, the kinetics, and the single-molecule interaction forces involved in the binding of CaM to the conserved helical segments of Orai1 and Orai3. The results consistently indicated stepwise binding of two separate target peptides to the two lobes of CaM. An unparalleled high affinity was found when two Orai peptides were dimerized or immobilized at high lateral density, thereby mimicking the close proximity of the N-termini in native Orai oligomers. The analogous experiments with smooth muscle myosin light chain kinase (smMLCK) showed only the expected 1:1 binding, confirming the validity of our methods.

Use of monolithic supports for high-throughput protein and peptide separation in proteomics.

The exclusive properties of monolithic supports enable fast mass transfer, high porosity, low back pressure, easy preparation process and miniaturisation, and the availability of different chemistries make them particularly suitable materials for high-throughput (HTP) protein and peptide separation. In this review recent advances in monolith-based chromatographic supports for HTP screening of protein and peptide samples are presented and their application in HTP sample preparation (separation, enrichment, depletion, proteolytic digestion) for HTP proteomics is discussed. Development and applications of different monolithic capillary columns in HTP MS-based bottom-up and top-down proteomics are overviewed. By discussing the chromatographic conditions and the mass spectrometric data acquisition conditions an attempt is made to present currently demonstrated capacities of monolithic capillary columns for HTP identification and quantification of proteins and peptides from complex biological samples by MS-based proteomics. Some recent advances in basic monolith technology of importance for proteomics are also discussed.

Identification of Plant Nuclear Proteins Based on a Combination of Flow Sorting, SDS-PAGE, and LC-MS/MS Analysis.

In the plant nucleus, the majority of cellular DNA content is stored and maintained. This makes this highly specialized organelle the major coordinator of almost all essential processes in plant cells such as transcription, DNA replication, and repair. None of these biological pathways can be fully understood without a comprehensive characterization of nuclear proteins. Nevertheless, the interest of the proteomic community in the plant nuclear proteome has been very limited so far. This is probably due to the high integrity of plant cell, presence of many interfering metabolites, and considerable endogenous proteolytic activity which make the sample preparation problematic. Hereby, we describe a novel protocol for the high-throughput plant nuclear protein identification that combines a flow cytometric sorting of formaldehyde-fixed nuclei with protein and peptide separation and their subsequent LC-MS/MS analysis.