Mitigation of signal suppression caused by the use of trifluoroacetic acid in liquid chromatography mobile phases during liquid chromatography/mass spectrometry analysis via post-column addition of ammonium hydroxide.

A method has been developed to reduce the mass spectrometric ion signal suppression associated with the use of TFA as an additive in LC mobile phases. Through post-column infusion of diluted NH(4)OH solution to LC eluents, the ammonium ion introduced causes the neutral analyte-TFA ion pair to dissociate which consequently releases the protonated analyte as free ions into the gas phase (through regular electrospray ionization mechanisms). An ion signal improvement from 1.2 to 20 times for a variety of compounds had been achieved through the application of this method. The molar ratios of NH(4)OH:TFA which result in a reduction of signal suppression were determined to be between 0.5:1 and 50:1. In addition, it was shown that this NH(4)OH infusion method could reduce the level of doubly-charged species and the product ions formed via in-source collision. The use of diluted NH(4)OH solution is favorable since it is compatible with mass spectrometry analysis, and it is applicable in both positive and negative-ion generation mode.

Comparison of HPLC/ESI-FTICR MS versus MALDI-TOF/TOF MS for glycopeptide analysis of a highly glycosylated HIV envelope glycoprotein.

Defining the structures and locations of the glycans attached on secreted proteins and virus envelope proteins is important in understanding how glycosylation affects their biological properties. Glycopeptide mass spectrometry (MS)-based analysis is a very powerful, emerging approach to characterize glycoproteins, in which glycosylation sites and the corresponding glycan structures are elucidated in a single MS experiment. However, to date there is not a consensus regarding which mass spectrometric platform provides the best glycosylation coverage information. Herein, we employ two of the most widely used MS approaches, online high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC/ESI-MS) and offline HPLC followed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), to determine which of the two approaches provides the best glycosylation coverage information of a complex glycoprotein, the group M consensus HIV-1 envelope, CON-S gp140DeltaCFI, which has 31 potential glycosylation sites. Our results highlight differences in the informational content obtained between the two methods such as the overall number of glycosylation sites detected, the numbers of N-linked glycans present at each site, and the type of confirmatory information obtained about the glycopeptide using MS/MS experiments. The two approaches are quite complementary, both in their coverage of glycopeptides and in the information they provide in MS/MS experiments. The information in this study contributes to the field of mass spectrometry by demonstrating the strengths and limitations of two widely used MS platforms in glycoprotein analysis.

Glycopeptide analysis by mass spectrometry.

Glycosylation is one of the most important post-translational modifications found in nature. Identifying and characterizing glycans is an important step in correlating glycosylation structure to the glycan's function, both in normal glycoproteins and those that are modified in a disease state. Glycans on a protein can be characterized by a variety of methods. This review focuses on the mass spectral analysis of glycopeptides, after subjecting the glycoprotein to proteolysis. This analytical approach is useful in characterizing glycan heterogeneity and correlating glycan compositions to their attachment sites on the protein. The information obtained from this approach can serve as the foundation for understanding how glycan compositions affect protein function, in both normal and aberrant glycoproteins.

Glycosylation site-specific analysis of HIV envelope proteins (JR-FL and CON-S) reveals major differences in glycosylation site occupancy, glycoform profiles, and antigenic epitopes' accessibility.

The HIV-1 envelope (Env) is a key determinant in mediating viral entry and fusion to host cells and is a major target for HIV vaccine development. While Env is typically about 50% glycan by mass, glycosylation sites are known to evolve, with some glycosylation profiles presumably being more effective at facilitating neutralization escape than others. Thus, characterizing glycosylation patterns of Env and native virions and correlating glycosylation profiles with infectivity and Env immunogenicity are necessary first steps in designing effective immunogens. Herein, we describe a mass spectrometry-based strategy to determine HIV-1 Env glycosylation patterns and have compared two mammalian cell expressed recombinant Env immunogens, one a limited immunogen and one that induces cross-clade neutralizing antibodies. We have used a glycopeptide-based mass mapping approach to identify and characterize Env's glycosylation patterns by elucidating which sites are utilized and what type of glycan motif is present at each glycosylation site. Our results show that the immunogens displayed different degrees of glycosylation as well as a different characteristic set of glycan motifs. Thus, these techniques can be used to (1) define glycosylation profiles of recombinant Env proteins and Env on mature virions, (2) define specific carbohydrate moieties at each glycosylation site, and (3) determine the role of certain carbohydrates in HIV-1 infectivity and in modulation of Env immunogenicity.

Chromatofocusing fails to separate hFSH isoforms on the basis of glycan structure.

Follicle-stimulating hormone (FSH) glycosylation is regulated by feedback from the gonads, resulting in an array of glycans associated with FSH preparations derived from pools of pituitary or urine extracts. FSH glycosylation varies due to inhibition of FSHbeta N-glycosylation, elaboration of 1-4 branches possessed by mature N-glycans, and the number and linkage of terminal sialic acid residues. To characterize FSH glycosylation, FSH isoforms in pituitary gland extracts and a variety of physiological fluids are commonly separated by chromatofocusing. Variations in the ratios of immunological and biological activities in the resulting FSH isoform preparations are generally attributed to changes in glycosylation, which are most often defined in terms of sialic acid content. Using Western blotting to assess human FSHbeta glycosylation inhibition revealed 30-47% nonglycosylated hFSHbeta associated with four of six hFSH isoform preparations derived by chromatofocusing. Glycopeptide mass spectrometry assessment of glycan branching in these isoforms extensively characterized two N-glycosylation sites, one at alphaAsn52, the critical glycan for FSH function, and the other at betaAsn24. With two to four N-glycans per FSH molecule, many combinations of charges distributed over these sites can provide the same isoelectric point. Indeed, several glycans were common to all isoform fractions that were analyzed. There was no trend showing predominantly monoantennary glycans associated with the high-pI fractions, nor were predominantly tri- and tetra-antennary glycans associated with low-pI fractions. Thus, differences in receptor binding activity could not be associated with any specific glycan type or location in the hormone. FSH aggregation was associated with reduced receptor binding activity but did not affect immunological activity. However, as gel filtration indicated sufficient heterodimer was present in each isoform preparation to generate complete inhibition curves, the near total loss of receptor binding activity in several preparations could not be explained by aggregation alone, and the mechanism remains unknown.

Application of the statistical test of equivalent pathways (STEP) method to the triple quadrupole mass spectrometer.

Recently, we demonstrated a new method, STEP (Statistical Test of Equivalent Pathways) analysis, which differentiates first-generation product ions (primary product ions) from second-generation product ions (secondary product ions) obtained in tandem mass spectrometric (MS/MS) experiments on a quadrupole ion trap mass spectrometer. The study presented here defines how to adapt the STEP method to a more routinely used mass analyzer, the triple quadrupole. New ion activation conditions were developed to adapt the STEP method to the triple quadrupole mass spectrometer using peptides and carbohydrates. The application of this method to the triple quadrupole is useful because it provides an efficient approach to differentiate primary and secondary ions on this instrument. Out of the total number of ions that were subjected to the STEP analysis, this method correctly identified 96% of ions as primary or secondary, indicating that this analysis is effective for carbohydrates and peptides undergoing collision-induced dissociation (CID) on a triple quadrupole mass spectrometer.

Simplification of mass spectral analysis of acidic glycopeptides using GlycoPep ID.

Mass spectral analysis is an increasingly common method used to characterize glycoproteins. When more than one glycosylation site is present on a protein, obtaining MS data of glycopeptides is a highly effective way of obtaining glycosylation information because this approach can be used to identify not only what the carbohydrates are but also at which glycosylation site they are attached. Unfortunately, this is not yet a routine analytical approach, in part because data analysis can be quite challenging. We are developing strategies to simplify this analysis. Presented herein is a novel mass spectrometry technique that identifies the peptide moiety of either sulfated, sialylated, or both sialylated and sulfated glycopeptides. This technique correlates product ions in collision-induced dissociation (CID) experiments of suspected glycopeptides to a peptide composition using a newly developed web-based tool, GlycoPep ID. After identifying the peptide portion of glycopeptides with GlycoPep ID, the process of assigning the rest of the glycopeptide composition to the MS data is greatly facilitated because the "unknown" portion of the mass assignment that remains can be directly attributed to the carbohydrate component. Several examples of the utility and reliability of this method are presented herein.

GlycoPep DB: a tool for glycopeptide analysis using a "Smart Search".

Mass spectrometry is emerging as a versatile analytical tool for profiling glycan and glycopeptide structures. While the interpretation of MS data remains a challenging and difficult task, substantial efforts have been made to develop informatics tools to alleviate MS data interpretation. Here, we present a web-based tool, GlycoPep DB, designed to facilitate compositional assignment for glycopeptides by comparing experimentally measured masses to all calculated glycopeptide masses from a carbohydrate database with N-linked glycans. GlycoPep DB is an advance over current tools to assign N-linked glycans because it uses a concept of "smart searching", where only biologically relevant carbohydrate compositions are searched, when matching carbohydrate compositions with the MS data making glycopeptide compositional assignment more efficient. This is in contrast to currently used tools, where many implausible glycan structures are present in the search output, but fewer biologically relevant glycan motifs are predicted. The utility of GlycoPep DB is illustrated in the analysis of glycopeptides derived from a proteolytic digest of follicle stimulating hormone.

Comparative glycomics of the glycoprotein follicle stimulating hormone: glycopeptide analysis of isolates from two mammalian species.

Follicle stimulating hormone (FSH) is one of the important hormones that regulate gonadal functions. This hormone is glycosylated, and the glycans greatly influence the biological properties. In the present study the negatively charged glycopeptides of equine and human pituitary follicle stimulating hormone (eFSH and hFSH) have been characterized in a glycosylation site-specific manner using FT-ICR-MS and Edman sequencing. The characteristic pattern of glycan distribution at each glycosylation site has been deduced and compared between horse and human FSH preparations. The data suggest that site-specific differences exist between glycoforms of human and equine FSH. For instance, except for one site in the beta subunit (Asn7) of hFSH all other sites in both species have sulfated glycoforms. Also, glycoforms at Asn52 of hFSH are all complex type, whereas in eFSH, both complex and hybrid structures exist at this site. There is also a higher percentage of sulfated glycans in the latter site compared to the former. This is the first study that characterizes the glycans from this hormone in a glycosylation site-specific manner, and these data can be used to begin correlative studies between glycosylation structure and hormone function.

Method for characterizing sulfated glycoproteins in a glycosylation site-specific fashion, using ion pairing and tandem mass spectrometry.

Structural analysis of sulfated glycans is essential in understanding their biological significance. Here, we present a new approach to characterize sulfated glycans present on glycoproteins. The analysis is performed on glycopeptides, so information about the sulfated species is obtained in a glycosylation site-specific manner. This method employs an ion-pairing reagent to stabilize the SO3 group of the glycopeptide, allowing useful information to be obtained during MS/MS experiments. The amount of structural information obtained from (+)ESI-MS/MS of the ion-pair complexes for sulfated glycopeptides of equine thyroid stimulating hormone is compared with information obtained by (-)ESI-MS/MS of the underivatized, sulfated glycopeptides. The results indicate that this new method provides detailed insights into the sequence, branching, and type of N-glycans present, compared to analysis via (-)ESI-MS/MS.

STEP (Statistical Test of Equivalent Pathways) analysis: a mass spectrometric method for carbohydrates and peptides.

We have recently developed a new mass spectrometry method, the STEP (statistical test of equivalent pathways) analysis that uses ion abundances in two tandem mass spectrometry experiments to obtain genealogy information about product ions present in mass spectra. The method requires minimal sample, and it can be performed using a conventional quadrupole ion trap mass spectrometer. To obtain genealogy information, STEP ratios are calculated by comparing the relative abundances of product ions in two MS/MS experiments. These ratios are directly related to the origin of the product ions. Product ions that result directly from the precursor ion always have STEP ratios that are

Reductive amination of carbohydrates using NaBH(OAc)3.

An improved protocol for reductive amination of carbohydrates is developed. This derivatization facilitates the detection of oligosaccharides in HPLC-UV and mass spectrometric applications by enhancing the signal of the carbohydrates. In this study, reductive amination was achieved using NaBH(OAc)3. This reducing agent is an attractive alternative to the toxic, but extensively used reducing agent, NaBH3CN. Several types of carbohydrates were successfully derivatized using NaBH(OAc)3, and the results obtained from this protocol were compared with those obtained with NaBH(OAc)3. Both reducing agents were equally effective in side-by-side analysis. Two purification strategies (purification by zip-tip and HPLC) were implemented and the instrumental limit of detection of each method was compared. The detection limit was approximately 1,000 times lower when the purification was done using HPLC, compared to using the zip-tip. Since the derivatization by-products in this protocol are not toxic, MS analysis also could also be performed directly, without purification. The MS/MS data of derivatized and underivatized oligosaccharides were acquired as well. The derivatized oligosaccharides produce more easily interpretable product ions than underivatized oligosaccharides.