Alex Apffel

Enhanced sensitivity for peptide mapping with electrospray liquid chromatography-mass spectrometry in the presence of signal suppression due to trifluoroacetic acid-containing mobile phases

A method is described for improving the sensitivity of peptide mapping with electrospray liquid chromatography--mass spectrometry using trifluoroacetic acid (TFA) containing HPLC mobile phases. The signal suppressing effects of TFA are shown to be due to the combined effect of ion-pairing and surface tension modifications. The post-column addition of a propionic acid-2-propanol (75:25, v/v) in a 1:2 proportion with the HPLC mobile phase counteracts the deleterious effects of TFA resulting in 10-100 x improvement of the signal-to-noise ratio. The system described introduces total HPLC flow (plus additive) directly into the electrospray source without splitting. Using 2.1 mm I.D. HPLC columns, minimum detectable quantities are below 40 pmol total protein. As examples, separations of proteolytic enzyme digests of several proteins are shown using standard HPLC conditions, comparing results with and without the addition of propionic acid. The application of the technique is shown in more depth in the identification of oxidative modification sites in glutamine synthetase. In this application, the enhanced sensitivity allowed location of a modified residue by comparison endoproteinase Lys C digest of native and oxidized forms of the protein without extensive sample preparation or concentration. A third application demonstrates the identification of glycosylation sites in an endoproteinase Arg C digest of single-chain plasminogen activator through the use of in-source collisionally induced dissociation.

Analysis of Oligonucleotides by HPLC-Electrospray Ionization Mass Spectrometry.

A new interface procedure has been developed that allows, for the first time, the high-efficiency analysis of synthetic oligonucleotides up to 75 bases by reversed-phase HPLC and on-line electrospray ionization mass spectrometry. For oligonucleotides up to 30 bases in length, single-base resolution can be obtained with low levels of cation adduct formation in the negative ion electrospray mass spectra. A key part of the method uses 1,1,1,3,3,3-hexafluoro-2-propanol as an additive to the HPLC mobile phase, adjusted to pH 7.0 with triethylamine. This novel additive results in both good HPLC separation and efficient electrospray ionization. The broad potential of this new method is demonstrated for synthetic homopolymers of thymidine (PolyT), fragments based on the pBR322 plasmid sequence, and phosphorothioate ester antisense oligonucleotides. This approach will be of particular utility for the characterization of DNA probes and PCR primers and quality control of antisense compounds such as phosphorothioates and their metabolites, as well as of materials used in clinical trials.

Signal enhancement for gradient reverse-phase high-performance liquid chromatography-electrospray ionization mass spectrometry analysis with trifluoroacetic and other strong acid modifiers by postcolumn addition of propionic acid and isopropanol

Trifluoroacetic acid (TFA) and other volatile strong acids, used as modifiers in reverse-phase high-performance liquid chromatography, cause signal suppression for basic compounds when analyzed by electrospray ionization mass spectrometry (ESI-MS). Evidence is presented that signal suppression is caused by strong ion pairing between the TFA anion and the protonated sample cation of basic sample molecules. The ion-pairing process “masks” the protonated sample cations from the ESI-MS electric fields by rendering them “neutral. ” Weakly basic molecules are not suppressed by this process. The TFA signal suppression effect is independent from the well-known spray problem that electrospray has with highly aqueous solutions that contain TFA. This previously reported spray problem is caused by the high conductivity and surface tension of aqueous TFA solutions. A practical method to enhance the signal for most basic analytes in the presence of signal-suppressing volatile strong acids has been developed. The method employs postcolumn addition of a solution of 75% propionic acid and 25% isopropanol in a ratio 1:2 to the column flow. Signal enhancement is typically 10–50 times for peptides and other small basic molecules. Thus, peptide maps that use ESI-MS for detection can be performed at lower levels, with conventional columns, without the need to use capillary chromatography or reduced mass spectral resolution to achieve satisfactory sensitivity. The method may be used with similar results for heptafluorobutyric acid and hydrochloric acid. A mechanism for TFA signal suppression and signal enhancement by the foregoing method, is proposed.

New procedure for the use of high-performance liquid chromatography–electrospray ionization mass spectrometry for the analysis of nucleotides and oligonucleotides

Abstract A method is described which allows the combination of high-performance liquid chromatography (HPLC) and electrospray ionization mass spectrometry for the analysis of nucleotides and oligonucleotides without compromising the performance of either technique. The essential feature of the method uses 1,1,1,3,3,3-hexafluoro-2-isopropanol as an additive to the HPLC mobile phase. This novel additive results in both good HPLC separation and efficient negative ion mode electrospray ionization. The method is demonstrated for oligonucleotides samples such as synthetic homopolymers of thymidine (PolyT), of fragments based on the pBR322 plasmid sequence and analysis of phosphorothioate ester antisense oligonucleotides. The differentiation of phosphorylation states of natural nucleotides as well as nucleotide analogues, such as ziduvodine (AZT), is also demonstrated.

α-arrestins Aly1 and Aly2 Regulate Intracellular Trafficking in Response to Nutrient Signaling

Arrestins, known regulators of endocytosis, take on novel functions in nutrient-regulated endosomal recycling. Yeast α-arrestins, Aly1 and Aly2, redistribute the Gap1 permease from endosomes to the cell surface and interact with clathrin/AP-1. Aly2 is regulated by the Npr1 kinase and acts through mechanisms distinct from Aly1.

Quantitation and linearity for particle-beam liquid chromatography-mass spectrometry

Abstract Quantitative performance for a particle-beam liquid chromatography-mass spectrometry system is evaluated with particular attention to non-linear behavior at low concentrations. A mathematical model for the non-linear behavior is proposed and shown to be in agreement with experimental data. The effects of 10 high-performance liquid chromatography mobile phase additives and 24 analytical probes on the linearity are shown. Although certain combinations of probes and additives show improved linear response, no single additive appears to completely alleviate the non-linear behavior as has been suggested by earlier work.

Effect of electric field on liquid chromatographic separation of peptide digests. Combining capillary separation techniques.

A system is described which allows operation of a range of capillary based liquid phase separations including capillary electrophoresis, isocratic and gradient capillary electrochromatography, isocratic and gradient capillary liquid chromatography and electrically assisted gradient capillary liquid chromatography. The system was coupled to electrospray ionization mass spectrometry in the electrically assisted capillary liquid chromatography mode to investigate the effect of applied voltage on the selectivity in peptide mapping separations. Analyses were performed on tryptic digests of recombinant human growth hormone and tissue plasminogen activator. The results show a small but useful effect on selectivity that can be used to fine tune specific separations.

Use of on-line mass spectrometric detection in capillary electrochromatography.

Capillary electrochromatography (CEC) is a liquid phase analytical separation technique that is generally carried out with packed capillary columns by electroosmotically driven mobile phase at high electric field strength. The analytes are separated by virtue of the differences in their distribution between the mobile and stationary phases and, if charged in their electrophoretic mobilities as well. It is thus considered a hybrid of liquid chromatography and capillary electrophoresis and is expected to combine the high peak efficiency of capillary zone electrophoresis (CZE) with the versatility and loading capacity of HPLC. This review explores the potential use of on-line mass spectrometric detection for CEC. It discusses key design issues that focus on the physical and electrical arrangement of the CEC column with respect to the electrospray orifice inlet. The salient features of the sheathless, sheath flow and liquid junction interfaces that are frequently employed while coupling a CEC column to an electrospray ionization mass spectrometry system are also highlighted. Possible configurations of the CEC column outlet that would obviate the need for pressurizing the capillary column are also presented. While coupling CEC with MS both the nature of the interface and the configuration of the column outlet will determine the optimal arrangement. The review also discusses bandspreading that occurs when a connecting tube is employed to transfer mobile phase from the column outlet to the atmospheric region of the electrospray source with a concomitant loss in sensitivity. Selected examples that highlight the potential of this technique for a wide range of applications are also presented.

Windowed mass selection method: a new data processing algorithm for liquid chromatography–mass spectrometry data

Abstract A number of preprocessing methods are tested on liquid chromatography–mass spectrometry (LC–MS) peptide map data, to determine the best and most efficient way to improve the signal to noise ratio in the data, especially at low analyte concentrations. Three methods are investigated, including an algorithm named “sequential paired covariance” (SPC), which was recently reported. An improvement to this algorithm is also reported here. This new, improved method, named the “windowed mass selection method” (WMSM), is shown to effectively eliminate random noise that occurs in the data. This method is shown to be particularly useful in improving signal to noise ratios in both chromatographic and mass spectra for data acquired in peptide mapping of recombinant DNA derived proteins.

The Use of Multidimensional Liquid-Phase Separations and Mass Spectrometry for the Detailed Characterization of Posttranslational Modifications in Glycoproteins

The goal of characterization of the proteome, while challenging in itself, is further complicated by the microheterogeneity introduced by posttranslational modifications such as glycosylation. A combination of liquid chromatography (LC), capillary electrophoresis (CE), and mass spectrometry (MS) offers the advantages of unique selectivity and high efficiency of the separation methods combined with the mass specificity and sensitivity of MS. In the current work, the combination of liquid-phase separations and mass spectrometry is demonstrated through the on-line coupling of electrospray ionization mass spectrometry (ESI-MS) and off-line coupling with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF-MS). LC/ESI-MS yields real-time results while maintaining the separation obtained from the LC analysis. CE/MALDI TOF-MS offers high-mass detection and extremely low detection limits. The unique separation selectivity of CE relative to reversed-phase HPLC separations of the members of a glycopeptide family was used to develop an integrated multidimensional analysis achieved by the off-line coupling of LC, CE, and MALDI TOF-MS. To demonstrate the applicability of these techniques to the characterization of the heterogeneity of posttranslational modifications present in glycoproteins, we will report on the study of the glycoforms present in a N-linked site in a single-chain plasminogen activator (DSPAα1).