Optimization of peptide separations in reversed-phase HPLC: Isocratic versus gradient elution

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.

An improved approach to hydrophilic interaction chromatography of peptides: salt gradients in the presence of high isocratic acetonitrile concentrations

Hydrophilic interaction chromatography (HILIC) for separations of peptides has been employed infrequently, particularly considering that this technique was introduced over 20 years ago. The present manuscript describes a radical departure from the traditional HILIC elution approach, where separations are achieved via increasing salt (sodium perchlorate) gradients in the presence of high isocratic concentrations (>80%) of acetonitrile, denoted HILIC/SALT. This initial study compared to reversed-phase chromatography (RPC), HILIC and HILIC/SALT for the separation of mixtures of synthetic peptide standards varying in structure (amphipathic α-helix, random coil), length (10-26 residues), number of positively charged residues (+1 to +11) and hydrophilicity/hydrophobicity. Results showed a marked superiority of the HILIC/SALT approach compared to traditional HILIC and excellent complementarity to RPC for peptide separations. We believe these initial results offer a new dimension to HILIC, enabling it to transform from an occasional HPLC approach for peptide separations to a more generally applicable method.

Design of peptide standards with the same composition and minimal sequence variation to monitor performance/selectivity of reversed-phase matrices

The present manuscript extends our de novo peptide design approach to the synthesis and evaluation of a new generation of reversed-phase HPLC peptide standards with the same composition and minimal sequence variation (SCMSV). Thus, we have designed and synthesized four series of peptide standards with the sequences Gly-X-Leu-Gly-Leu-Ala-Leu-Gly-Gly-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 1) or contains a free α-amino group (Series 3); and Gly-Gly-Leu-Gly-Gly-Ala-Leu-Gly-X-Leu-Lys-Lys-amide, where the N-terminal is either N(α)-acetylated (Series 2) or contains a free α-amino group (Series 4). In this initial study, the single substitution position, X, was substituted with alkyl side-chains (Ala Collapse

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MESH Headings

• Amino Acid Sequence
• Chromatography, High Pressure Liquid/standards
• Chromatography, Reverse-Phase/standards
• Peptides/chemistry
• Reference Standards

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Grants

• R01 GM061855 NIGMS NIH HHS
• R01 GM061855-10 NIGMS NIH HHS
• R01 GM61855 NIGMS NIH HHS

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Affiliation(s)

Colin T. Mant Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA
Robert S. Hodges Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, CO 80045, USA

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Bioanalytical approaches to analyzing peptides and proteins by LC–MS/MS

Peptides and proteins have been utilized as therapeutic agents for over 40 years. Traditional approaches to quantify these molecules in biological matrices have utilized immunoassay approaches that can be time inefficient, lack assay specificity and have limited analytical ranges. The advances in sample preparation technologies, chromatographic systems and their chemistries, mass spectrometers and their software over the last decade have meant that LC–MS/MS approaches to peptide and protein quantification are feasible and can overcome the problems associated with quantification by immunoassay. In this article we present an overview of the challenges and approaches to overcome them when performing quantitative bioanalysis of peptides and proteins by LC–MS/MS.

Preparative reversed-phase high-performance liquid chromatography collection efficiency for an antimicrobial peptide on columns of varying diameters (1mm to 9.4mm I.D.)

The present study examines the effect of reversed-phase high-performance liquid chromatography (RP-HPLC) column diameter (1mm to 9.4mm I.D.) on the one-step slow gradient preparative purification of a 26-residue synthetic antimicrobial peptide. When taken together, the semi-preparative column (9.4mm I.D.) provided the highest yields of purified product (an average of 90.7% recovery from hydrophilic and hydrophobic impurities) over a wide range of sample load (0.75-200mg). Columns with smaller diameters, such as narrowbore columns (150x2.1mm I.D.) and microbore columns (150x1.0mm I.D.), can be employed to purify peptides with reasonable recovery of purified product but the range of the crude peptide that can be applied to the column is limited. In addition, the smaller diameter columns require more extensive fraction analysis to locate the fractions of pure product than the larger diameter column with the same load. Our results show the excellent potential of the one-step slow gradient preparative protocol as a universal method for purification of synthetic peptides.

One-step purification of a recombinant protein from a whole cell extract by reversed-phase high-performance liquid chromatography

We have developed a one-step facile, flexible and readily scalable purification method for a recombinant protein, TM 1-99 (113 amino acid residues; 12,837 Da) based on reversed-phase high-performance liquid chromatography (RP-HPLC) from an E. coli cell lysate. Following cell lysis, the cell contents were extracted with 0.1% aqueous trifluoroacetic acid (TFA), applied directly under conditions of high sample load to a narrow bore RP-HPLC C(8) column (150 mm x 2.1 mm I.D.) and eluted by a shallow gradient of acetonitrile (0.1%/min). Loads of 23 and 48 mg of lyophilized crude cell extract produced 2.4 and 4.2mg of purified product (>94% pure), respectively, at >94% recovery. Our results show the excellent potential of one-step RP-HPLC for purification of recombinant proteins from cell lysates, where high yields of purified product and greater purity are achieved compared to affinity chromatography. Such an approach was also successful in purifying just trace levels (<0.1% of total contents of crude sample) of TM 1-99 from a cell lysate.

Temperature profiling of polypeptides in reversed-phase liquid chromatography

The present study sets out to extend the utility of reversed-phase liquid chromatography (RP-HPLC) by demonstrating its ability to monitor dimerization and unfolding of de novo designed synthetic amphipathic alpha-helical peptides on stationary phases of varying hydrophobicity. Thus, we have compared the effect of temperature (5-80 degrees C) on the RP-HPLC (C8 or cyano columns) elution behaviour of mixtures of peptides encompassing amphipathic alpha-helical structure, amphipathic alpha-helical structure with L- or D-substitutions or non-amphipathic alpha-helical structure. By comparing the retention behaviour of the helical peptides to a peptide of negligible secondary structure (a random coil), we rationalize that "temperature profiling" by RP-HPLC can monitor association of peptide molecules, either through oligomerization or aggregation, or monitor unfolding of alpha-helical peptides with increasing temperature. We believe that the conformation-dependent response of peptides to RP-HPLC under changing temperature has implications both for general analysis and purification of peptides but also for the de novo design of peptides and proteins.

Preparative reversed-phase liquid chromatography of proteins from rabbit skeletal troponin, a multi-protein complex

A reversed-phase high-performance liquid chromatography protocol for purification of all proteins in a multi-protein (TnI, TnC, TnT, tropomyosin) complex from rabbit skeletal muscle has been developed, enabling efficient purification of sample amounts ranging from 43 mg of protein complex on a standard analytical column, to 1400 mg on a column of 21.2 mm I.D. and finally, to 5700 mg on a column of 50 mm I.D. Due to problems associated with scale-up procedures for these proteins (e.g. aggregation and/or solubility issues), an initial sample fractionation was devised whereby 50% of the TnC component was precipitated with acetonitrile prior to sample introduction on the RPLC column. By subsequently taking advantage of sample overload conditions to enhance the displacement effect between sample components, coupled with very slow gradient conditions (0.1% acetonitrile/min), we were able to achieve excellent protein separations at high yields of purified proteins.

On-line analysis by capillary separations interfaced to an ion trap storage/reflectron time-of-flight mass spectrometer

The interface of high-resolution capillary separation methods to time-of-flight mass spectrometry (TOF-MS) has generated considerable interest since TOF can provide the rapid and sensitive detection required by high resolution separations. In recent years, our laboratory has developed a variety of high-resolution capillary separation methods interfaced to TOF-MS via an ion trap storage/reflectron time-of-flight (IT/reTOF) instrument. Using this hybrid configuration, detection of fast separations at very low detection levels has been successfully performed for on-line separations of peptides and protein digests using electrospray ionization. In this report, we review the current status in our laboratory of interfacing high-performance liquid chromatography, capillary electrophoresis, and capillary electrochromatography to an IT/reTOF-MS instrument and various applications that have been developed involving this technology.

Effect of mobile phase additives on peptide retention in reversed-phase chromatography with pellicular and totally porous sorbents

The effect of two mobile phase additives, trifluoroacetic acid and phosphoric acid, on the energetics of peptide retention in reversed-phase chromatography was investigated using Hy-Tach C18 micropellicular and Vydac C4 and C18 totally porous stationary phases. The effect of the relatively low phase ratio of columns packed with micropellicular sorbents was also examined. The logarithmic retention factors, of two model peptides, Ac-RGGGGLGLGK-amide and Ac-RGAGGLGLGK-amide, were evaluated with different columns and additives in a practical range of eluent strength. The dependence of the logarithmic retention factor on the concentration of acetonitrile in the mobile phase was linear in all cases. The higher sensitivity of the retention to the organic modifier concentration in the case of the Hy-Tach C18 column is attributed to the relatively low phase ratio of this column. Pairwise plots of the logarithmic retention factors were linear. The plots of data obtained with the two additives has unit slopes and thus reveal homoenergetic retention behavior. On the other hand data obtained on two different columns manifest homeoenergetic retention, the slopes of plots are different from unity. The analysis has yielded consistent results and validated the assumption that the retention free energy can be divided into two components arising from mobile phase and stationary phase contributions. The approach also allowed an estimation of the relative phase ratios of the columns and the Vydac C18 column was found to have an 3 and 8 times higher phase ratio than the Vydac C4 and the Hy-Tech C18 column, respectively.

A comparative study of the interactions of synthetic peptides of the skeletal and cardiac troponin I inhibitory region with skeletal and cardiac troponin C

The cardiac and skeletal TnI inhibitory regions have identical sequences except at position 110 which contains Pro in the skeletal sequence and Thr in the cardiac sequence. The effect of the synthetic TnI inhibitory peptides [skeletal TnI peptide (104-115), cardiac TnI peptide (137-148), and a single Gly-substituted analogue at position 110] on the secondary structure of skeletal and cardiac TnC was investigated. The biphasic increases in ellipticity and tyrosine fluorescence were analyzed to determine the Ca2+ binding constants for the high- and low-affinity Ca2+ binding sites of TnC. Importantly, the skeletal and cardiac TnI peptides altered Ca2+ binding at the low-affinity sites of TnC, but the magnitude and direction of the pCa shifts depended on whether the peptides were bound to skeletal or cardiac TnC. For example, binding of skeletal TnI peptide to skeletal TnC (monitored by CD) caused a pCa shift of +0.30 unit such that a lower Ca2+ concentration was required to fill sites I and II, while binding of this peptide to cardiac TnC caused a pCa shift of -0.35 unit such that a higher Ca2+ concentration was required to fill site II. This is the first report of the alteration at the low-affinity regulatory sites (located in the N-terminal domain) by the skeletal TnI inhibitory peptide, even though the primary peptide binding site is located in the C-terminal domain of TnC, a finding which strongly indicates that there is communication between the two halves of the TnC molecule.(ABSTRACT TRUNCATED AT 250 WORDS)

Cation-exchange chromatography of peptides on poly(2-sulfoethyl aspartamide)-silica

A strong cation-exchange material, poly(2-sulfoethyl aspartamide)-silica (PolySULFOETHYL Aspartamide) was developed for purification and analysis of peptides by high-performance liquid chromatography. All peptides examined were retained at pH 3, even when the amino terminus was the only basic group. Peptides were eluted in order of increasing number of basic residues with a salt gradient. Capacity was high, as was selectivity and column efficiency. This new column material displays modest mixed-mode effects, allowing the resolution of peptides having identical charges at a given pH. The selectivity can be manipulated by the addition of organic solvent to the mobile phases; this increases the retention of some peptides and decreases the retention of others. The retention in any given case may reflect a combination of steric factors and non-electrostatic interactions. Selectivity was complementary to that of reversed-phase chromatography (RPC) materials. Excellent purifications were obtained by sequential use of PolySULFOETHYL Aspartamide and RPC columns for purification of peptides from crude tissue extracts. The new cation exchanger is quite promising as a supplement to RPC for general peptide chromatography.