Application of mobile phase additives to reduce metal-ion mediated adsorption of non-phosphorylated peptides in RPLC/MS-based assays

Liquid Chromatography Methods for Analysis of mRNA Poly(A) Tail Length and Heterogeneity

Messenger RNA (mRNA) is a new class of therapeutic compounds. The current advances in mRNA technology require the development of efficient analytical methods. In this work, we describe the development of several methods for measurement of mRNA poly(A) tail length and heterogeneity. Poly(A) tail was first cleaved from mRNA with the RNase T1 enzyme. The average length of a liberated poly(A) tail was analyzed with the size exclusion chromatography method. Size heterogeneity of the poly(A) tail was estimated with high-resolution ion-pair reversed phase liquid chromatography (IP RP LC). The IP RP LC method provides resolution of poly(A) tail oligonucleotide variants up to 150 nucleotide long. Both methods use a robust ultraviolet detection suitable for mRNA analysis in quality control laboratories. The results were confirmed by the LC-mass spectrometry (LC MS) analysis of the same mRNA sample. The poly(A) tail length and heterogeneity results were in good agreement.

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.

Liquid chromatography method for simultaneous quantification of ATP and its degradation products compatible with both UV-Vis and mass spectrometry

ATP and its degradation products are essential metabolic and signaling molecules. Traditionally, they have been quantified via high-performance liquid chromatography (HPLC) with UV-Vis detection while utilizing phosphate buffer mobile phase, but this approach is incompatible with modern mass detection. The goal of this study was to develop an ultra-performance liquid chromatography (UPLC) method free of phosphate buffer, to allow for analysis of adenine nucleotides with UV-Vis and mass spectrometry (MS) simultaneously. The final conditions used an Acquity HSS T3 premier column with a volatile ammonium acetate buffer to successfully separate and quantify ATP-related analytes in a standard mixture and in extracts from non-contracted and contracted mouse hindlimb muscles. Baseline resolution was achieved with all 10 metabolites, and a lower limit of quantification down to 1 pmol per inject was observed for most metabolites using UV-Vis. Therefore, this method allows for the reliable quantification of adenine nucleotides and their degradation products via UV-Vis and their confirmation and/or identification of unknown peaks via MS.

Evaluation of hybrid surface technology for the analysis of the B-group vitamins by LC-ESI-MS/MS

Recently, a novel hybrid surface technology (HST) has been developed to mitigate metal analyte adsorption in liquid chromatography. The HST provides a hybrid organic-inorganic surface on the metal fluidic path, from injection to detector and including the column frits and wall, to mitigate the interaction between analytes and metals. Here the impact of the HST on the analysis of B group vitamins using liquid chromatography coupled with electrospray tandem mass spectrometry (LC-ESI-MS/MS) has been evaluated. Significant improvements in analyte intensity, limit of quantification (LOQ), carry-over, and peak shape were observed using an LC-ESI-MS/MS system and column that incorporated the HST. The key observed improvements include a 3-10 times increase in sensitivity (providing a lower LOQ) for riboflavin, thiamine, nicotinamide, FMN, PLP, and 5MTHF, no carry-over, and a more symmetrical peak for thiamine. When applied to the analysis of B group vitamins in energy drinks and B vitamin dietary supplement samples, the HST system demonstrated excellent accuracy and repeatability.

Influence of metals in the column or instrument on performance in hydrophilic interaction liquid chromatography

A method is proposed for measuring the relative contribution of extracolumn and column effects to the detrimental interactions which occur between metal-sensitive solutes and the complete HPLC system. The method involves the substitution of a length of narrow bore silica tubing for the column and measuring the extracolumn contribution, which is subtracted from the total bandspreading measured with a column in place to yield the column contribution. The investigation focussed on HILIC separations, which have been relatively little studied compared with similar effects in RPLC. Metal-solute interactions can lead to tailing peaks and reduced sensitivity or even irreversible adsorption of particularly challenging solutes such as mono-, di- and triphosphorylated nucleotides, which show strong interactions between their phosphate groups and metals. A deactivated HILIC column, treated by a vapour deposition procedure gave generally good results when using high pH (pH 9.0) mobile phases, which suppress the effects of metals. The addition of metal complexing agents such as citrate at low millimolar concentration gave further improvements in peak shape at high pH, and even micromolar concentrations of citrate or medronic acid showed good results. These lower concentrations are more favourable for LC-MS. Addition of the higher concentration of citrate gave acceptable results for the nucleotides even at low pH (pH 3.0). With the standard UHPLC instrument used, loss of efficiency due to metal solute interactions was 25% or less, with most losses due to interactions with the column, although this result will depend on the condition and design of the instrument, which is easily assessed by the proposed procedure.

Approaches to liquid chromatography tandem mass spectrometry assessment of glyphosate residues in wine

The performance of two different analytical methodologies to investigate the presence of glyphosate (GLY) and aminomethylphosphonic acid (AMPA) residues in wine samples was evaluated. Transformation of compounds in their fluorene-9-methyloxycarbonyl derivatives permitted their separation under reversed-phase liquid chromatography with tandem mass spectrometry (LC-MS/MS) determination. Although the wine matrix severely impaired the efficiency of GLY derivatization, this drawback was solved using a molecularly imprinted sorbent for the previous, selective extraction of GLY and AMPA from wine. Alternatively, the use of a strong anionic exchange, polyvinyl alcohol-based LC column, turned to be the most effective alternative for direct determination of both compounds in diluted wine samples. The chromatographic behavior of this column and the magnitude of matrix effects observed during analysis of diluted wine samples were significantly affected by the composition of the mobile phase. Under final working conditions, this column permitted the separation of AMPA and the fungicide fosetyl (which shows common transitions in tandem MS/MS methods), it improved significantly the sample throughput versus extraction-derivatization-purification method, and it allowed the use of solvent-based calibration standards. Both analytical procedures provided similar limits of quantification (LOQs) for GLY (0.5-1.0 ng mL-1), while the multistep method was 8 times more sensitive to AMPA than the direct procedure. GLY residues stayed above method LOQs in 70% of the processed wines; however, concentrations measured in 95% of positive samples remained 100 times below the maximum residue limit (MRL) set for GLY in vinification grapes.

Mitigation of analyte loss on metal surfaces in liquid chromatography

The adsorptive loss of acidic analytes in liquid chromatography was investigated using metal frits. Repetitive injections of acidic small molecules or an oligonucleotide were made on individual 2.1 or 4.6 mm i.d. column frits. Losses were observed for adenosine 5'-(α,β-methylene) diphosphate, 2-pyridinol 1-oxide and the 25-mer phosphorothioate oligonucleotide Trecovirsen (GEM91) on stainless steel and titanium frits. Analyte adsorption was greatest at acidic pH due to the positive charge on the metal oxide surface. Analyte recovery increased when a series of injections was performed; this effect is known as sample conditioning. Nearly complete recovery was achieved when the metal adsorptive sites were saturated with the analyte. A similar effect was achieved by conditioning the frits with phosphoric, citric or etidronic acids, or their buffered solutions. These procedures can be utilized to mitigate analyte loss. However, the effect is temporary, as the conditioning agent is gradually removed by the running mobile phase. Metal frits modified with hybrid organic/inorganic surface technology were shown to mitigate analyte-to-metal surface interactions and improve recovery of acidic analytes. Quantitative recovery of a 15-35 mer oligodeoxythymidine mixture was achieved using column hardware modified with hybrid surface technology, without a need for column conditioning prior to analysis.

A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns

Reversed-phase HPLC is the most commonly applied peptide-separation technique in MS-based proteomics. Particle-packed capillary columns are predominantly used in nanoflow HPLC systems. Despite being the broadly applied standard for many years, capillary columns are still expensive and suffer from short lifetimes, particularly in combination with ultra-high-pressure chromatography systems. For this reason, and to achieve maximum performance, many laboratories produce their own in-house packed columns. This typically requires a considerable amount of time and trained personnel. Here, we present a new packing system for capillary columns enabling rapid, multiplexed column packing with pressures reaching up to 3000 bar. Requiring only a conventional gas pressure supply and methanol as the driving fluid, our system replaces the traditional setup of helium-pressured packing bombs. By using 10× multiplexing, we have reduced the production time to just under 2 min for several 50 cm columns with 1.9-µm particle size, speeding up the process of column production 40 to 800 times. We compare capillary columns with various inner diameters and lengths packed under different pressure conditions with our newly designed, broadly accessible high-pressure packing station.

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We present a newly designed high-pressure packing station for capillary columns.

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Detailed part lists and manufacturing instructions included.

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40 to 800 times faster packing of capillary columns for high-performance proteomics.

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Columns produced with the presented setup have state-of-the-art quality metrics.