Electrospray ionization protein separation

Electrospray ionization mass spectrometry (ESI-MS) is an analytical method for mass determination of ionized molecules. It is a commonly used method for soft ionization of peptides and proteins in quadmpole, ion-trap, or time-of-flight mass spectrometers. The ionization is performed by application of a high voltage to a stream of liquid emitted from a capillaty. The highly charged droplets are shrunk and the resulting peptide or protein ions are sampled and separated by the mass spectrometer. 

The effect of the buffer on the efficiency of electrospray ionization was mentioned earlier in Section 4.7.1. This is a good example of the dramatic effect that this may have - good chromatographic separation and ionization efficiency with formic, acetic and propionic acids, and good separation, although with complete suppression of ionization, with trifluoroacetic acid (TFA), the additive used for the protein application described previously. Post-column addition of propionic acid to the mobile phase containing TFA has been shown to reduce, or even... 

MALDI-ToF is a technique that allows the molecular weights of proteins and peptides to be determined. It is less susceptible to suppression effects than electrospray ionization and thus is able to be used for the direct analysis of mixtures. In the case of a crude tryptic digest, MALDI-ToF will provide a molecular weight profile of the polypeptides present without the analysis time being extended by the need to use some form of chromatographic separation. 

Wall, D. B Kachman, M. T Gong, S. Y. S Parus, S. J Long, M. W Lubman, D. M. (2001). Isoelectric focusing nonporous silica reversed-phase high-performance liquid chromatog-raphy/electrospray ionization time-of-flight mass spectrometry a three-dimensional liquid-phase protein separation method as applied to the human erythroleukemia cell-line. Rapid Commun Mass Sp. 15(18), 1649-1661. 

FIGURE 13.4 Total ion chromatograms from the ID LC/MS analysis of a yeast ribosomal protein fraction separated using 0.1% TFA (Panel a) and 0.1% formic acid (Panel b) as mobile phase modifiers. TFA produced narrower, more concentrated, peaks for mass analysis that did not overcome the significant electrospray ionization suppression associated with using this modifier for LC/MS studies, resulting in an overall reduction in component intensities. 

Because plasma and urine are both aqueous matrixes, reverse-phase or polar organic mode enantiomeric separations are usually preferred as these approaches usually requires less elaborate sample preparation. Protein-, cyclodextrin-, and macrocyclic glycopeptide-based chiral stationary phases are the most commonly employed CSPs in the reverse phase mode. Also reverse phase and polar organic mode are more compatible mobile phases for mass spectrometers using electrospray ionization. Normal phase enantiomeric separations require more sample preparation (usually with at least one evaporation-to-dryness step). Therefore, normal phase CSPs are only used when a satisfactory enantiomeric separation cannot be obtained in reverse phase or polar organic mode. 

Fang X, Yang L, Wang W, et al. Comparison of electrokinetics-based multidimensional separations coupled with electrospray ionization-tandem mass spectrometry for characterization of human salivary proteins. Anal. Chem. 2007 79 5785-5792. 

The ability to prepare monoliths within a mold of any shape was used by Lee et al. [128] who prepared monolithic ST-DVB microbeads within pulled fused silica needles and used them for the reversed-phase separation and on-line electrospray ionization mass spectrometry (ESI-MS) detection of proteins and peptides. As illustrated by Fig. 18, these monolithic microcolumns separated proteins far better than capillaries packed with commercial C18 silica or polymeric beads. 

Even if relatively new, HF FIFFF has been used to separate supramicrometer particles, proteins, water-soluble polymers, and synthetic organic-soluble polymers. Particle separation in HF FIFFF has recently been improved, reaching the level of efficiency normally achieved by conventional, rectangular FIFFF channels. With these channel-optimized HF FIFFF systems, separation speed and the resolution of nanosized particles have been increased. HF FIFFF has recently been examined as a means for off-line and on-line protein characterization by using the mass spectrometry (MS) through matrix-assisted laser desorption ionization time-of-flight mass spectrometry (M ALDl-TOF MS) and electrospray ionization (ESl)-TOF MS, as specific detectors. On-line HF FIFFF and ESl-TOF MS analysis has demonstrated the viability of fractionating proteins by HF FIFFF followed by direct analysis of the protein ions in MS [38]. 

The use and development of high-resolving separation techniques as well as highly accurate mass spectrometers is nowadays essential to solve the proteome complexity. Currently, more than a single electrophoretic or chromatographic step is used to separate the thousands of proteins found in a biological sample. This separation step is followed by analysis of the isolated proteins (or peptides) by mass spectrometry (MS) via the so-called soft ionization techniques, such as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) combined with the everyday more powerful mass spectrometers. Two fundamental analytical strategies can be employed the bottom-up and the top-down approach. 

At about the same time, our laboratory has reported the development and validation of an LC tandem MS assay for as much as six TKIs simultaneously. The proposed LC-MS/MS method allows the simultaneous determination of clinically relevant ranges of concentrations for the six major TKIs currently in use imatinib, dasatinib, nilotinib, sunitinib, sorafenib, and lapatinib [122], Plasma is purified by acetonitrile protein precipitation followed by reversed-phase chromatographic separation. Analyte quantification is performed by electrospray ionization-triple quadrupole mass spectrometry by selected reaction monitoring (SRM) detection using the positive mode. This was the first broad-range LC-MS/MS assay covering the major currently in-use TKIs. 

As a rule, a separation method should be used for both purification and concentration of the sample. The classic method for peptides and proteins is a reverse-phase liquid chromatography preparation of the sample, followed by a concentration step (often lyophiliza-tion) of the fraction of interest. During those steps performed on very small quantities of sample, loss on the sample can occur if care is not taken to avoid it. Lyophilization, for instance, can lead to the loss of the sample absorbed on the walls of the vial. The use of separation methods on-line with the mass spectrometer often are preferred. Micro- or nano-HPLC [32,33] and capillary electrophoresis [34], both coupled mainly to electrospray ionization/mass spectrometry (ESI-MS), are used more and more. 

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