Interlaboratory study on differential analysis of protein glycosylation by mass spectrometry: the ABRF glycoprotein research multi-institutional study 2012.

One of the principal goals of glycoprotein research is to correlate glycan structure and function. Such correlation is necessary in order for one to understand the mechanisms whereby glycoprotein structure elaborates the functions of myriad proteins. The accurate comparison of glycoforms and quantification of glycosites are essential steps in this direction. Mass spectrometry has emerged as a powerful analytical technique in the field of glycoprotein characterization. Its sensitivity, high dynamic range, and mass accuracy provide both quantitative and sequence/structural information. As part of the 2012 ABRF Glycoprotein Research Group study, we explored the use of mass spectrometry and ancillary methodologies to characterize the glycoforms of two sources of human prostate specific antigen (PSA). PSA is used as a tumor marker for prostate cancer, with increasing blood levels used to distinguish between normal and cancer states. The glycans on PSA are believed to be biantennary N-linked, and it has been observed that prostate cancer tissues and cell lines contain more antennae than their benign counterparts. Thus, the ability to quantify differences in glycosylation associated with cancer has the potential to positively impact the use of PSA as a biomarker. We studied standard peptide-based proteomics/glycomics methodologies, including LC-MS/MS for peptide/glycopeptide sequencing and label-free approaches for differential quantification. We performed an interlaboratory study to determine the ability of different laboratories to correctly characterize the differences between glycoforms from two different sources using mass spectrometry methods. We used clustering analysis and ancillary statistical data treatment on the data sets submitted by participating laboratories to obtain a consensus of the glycoforms and abundances. The results demonstrate the relative strengths and weaknesses of top-down glycoproteomics, bottom-up glycoproteomics, and glycomics methods.

Improved enrichment and proteomic identification of outer membrane proteins from a Gram-negative bacterium: focus on Caulobacter crescentus.

Efforts to characterize proteins found in the outer membrane (OM) of Gram-negative bacteria have been steadily increasing due to the promise of expanding our understanding of fundamental bacterial processes such as cell adhesion or cell wall biogenesis as well as the promise of finding potential vaccine- or drug-targets for virulent bacteria. We have developed a mass spectrometry-compatible experimental strategy that resulted in increased coverage of the OM proteome of a model organism, Caulobacter crescentus. The specificity of the OM enrichment step was improved by using detergent solubilization of the protein pellet, low-density cell culture conditions, and a surface-layer deficient cell line. Additionally, efficient gel-assisted digestion, high-resolution RP/RP-MS/MS, and rigorous bioinformatic analysis led to the identification of 234 proteins using strict identification criteria (≥ two unique peptides per protein; peptide false discovery rate <2%). Eighty-four of the detected proteins were predicted to localize to the OM or extracellular space. These results represent ~70% coverage of the predicted OM/extracellular proteome of C. crescentus. This analytical approach, which considers important experimental variables not previously explored in published OM protein studies, can be applied to other OM proteomic endeavors "as is" or with slight modification and should improve the large-scale study of this especially challenging subproteome.

Proteomic analysis of lipid raft-enriched membranes isolated from internal organelles.

The mitochondria-associated membrane (MAM) is a sub-region of the endoplasmic reticulum (ER) that facilitates crosstalk between the ER and mitochondria. The MAM actively influences vital cellular processes including Ca(2+) signaling and protein folding. Detergent-resistant microdomains (DRMs) may localize proteins to the mitochondria/MAM interface to coordinate these events. However, the protein composition of DRMs isolated from this region is not known. Lipid-raft enriched DRMs were isolated from a combined mitochondria/MAM sample and analyzed using two-dimensional reversed-phased tandem mass spectrometry. Strict post-acquisition filtering of the acquired data led to the confident identification 250 DRM proteins. The majority (58%) of the identified proteins are bona fide mitochondrial or ER proteins according to Gene Ontology annotation. Additionally, 74% of the proteins have previously been noted as MAM-resident or -associated proteins. Furthermore, ∼20% of the identified proteins have a documented association with lipid rafts. Most importantly, known internal LR marker proteins (inositol 1,4,5-trisphosphate receptor type 3, erlin-2, and voltage-dependent anion channel 1) were detected as well as most of the components of the mitochondrial/MAM-localized Ca(2+) signaling complex. Our study provides the basis for future work probing how the protein activities at the mitochondrion/MAM interface are dependent upon the integrity of these internal lipid-raft-like domains.

Testicular torsion alters the presence of specific proteins in the mouse testis as well as the phosphorylation status of specific proteins.

Testicular torsion followed by torsion repair induces an ischemia-reperfusion injury to the testis that can render the testis aspermatogenic. Previous results have demonstrated this loss of spermatogenesis to be the result of germ cell apoptosis induced by oxidative stress. The present work reports protein changes occurring in the mouse testis 24 hours after repair of a testicular torsion known to induce germ cell apoptosis and severe seminiferous impairment. Total proteins were extracted from sham-operated testes and testes having had 2-hour 720 degrees torsion 24 hours previously. Testicular proteins were separated by 2-dimensional electrophoresis and the resulting gel images were analyzed with image analysis software. Of the over 1100 proteins detected on the average gel, over 700 were consistently appearing in multiple gels, and those protein spot intensities were averaged within sham and torsion groups and compared between the 2 groups. Twenty-three proteins were consistently increased after torsion repair and 48 were decreased. Six proteins, 3 of which increased and 3 of which decreased after torsion repair, were identified by mass spectrometry. The 3 proteins that increased after torsion repair, beta2-tubulin and 2 isoforms of serum albumin, as well as the 3 proteins that decreased after torsion repair, vimentin, phosphoglycerate kinase, and t-complex protein 1beta, were for the most part associated with various aspects of cell stress responses. The number of proteins phosphorylated on tyrosine residues exceeded the number of proteins phosphorylated on serine/threonine residues, but among 6 stress-related proteins specifically examined for phosphorylation in sham testes and those examined after torsion repair, increases in threonine phosphorylation of c-Jun NH2 terminal kinase and activating transcription factor 2 were the most prominent. Knowing these proteins and the pathways to which they point will aid in the search for new therapies of oxidative stress in the testis.

Proteomic profiling of the surface-exposed cell envelope proteins of Caulobacter crescentus.

Biotinylation of intact cells, avidin enrichment of derivatized peptides, and shotgun proteomics were employed to reveal the composition of the surface-exposed proteome of the aquatic bacterium, Caulobacter crescentus. Ninety-one unique proteins were identified with the majority originating from the outer membrane, periplasm, and inner membrane, subcellular regions that comprise the Gram-negative bacterium cell envelope. Many of these proteins were described as 'conserved hypothetical protein' or 'hypothetical protein'; and so, the actual expression of these gene products was confirmed. Others did not have any known function or lacked annotation. However, this investigation of the Caulobacter surfaceome did reveal the unanticipated presence of a number of enzymes involved in protein degradation. BIOLOGICAL SIGNIFICANCE: The results presented here can provide a starting point for hypothesis-driven research projects focused on this bacterium in particular and centered on understanding Gram-negative cell architecture and outer membrane biogenesis broadly. The detected protein degradation enzymes anchored on or located within the outer membrane suggest that Caulobacter has nutrient sources larger than small molecules and/or further processes surface proteins once secreted to this location. Additionally, confirmation of outer membrane residency of those proteins predicted to be periplasmic or whose location prediction was not definitive could potentially elucidate the identities of Gram-negative specific anchorless surface proteins. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

In-depth proteomic analysis of mammalian mitochondria-associated membranes (MAM).

The endoplasmic reticulum (ER) and mitochondria communicate via contact sites known as mitochondria-associated ER membranes or MAM. The region has emerged as the primary area of Ca(2+) traffic between the two organelles, and as such, has been implicated in the regulation of protein folding, oxidative phosphorylation, and Ca(2+)-mediated apoptosis. In order to better understand biological processes and molecular functions at the MAM, we report a global mass spectrometry-based proteomic evaluation of the MAM obtained from mouse brain samples. Gel-assisted sample preparation in conjunction with our two-dimensional chromatography approach allowed for the identification of 1,212 high confidence proteins. Bioinformatic interrogation of this protein catalogue using Ingenuity Pathway Analysis revealed new potential connections between our list of MAM proteins and neurodegenerative diseases in addition to anticipated biological processes. Based on our results, we postulate that proteins of the MAM may play essential roles in dysfunctions responsible for several neurological disorders in addition to facilitating key cellular survival processes.

Aleuria Aurantia Lectin (AAL)-reactive immunoglobulin G rapidly appears in sera of animals following antigen exposure.

We have discovered an Aleuria Aurantia Lectin (AAL)-reactive immunoglobulin G (IgG) that naturally occurs in the circulation of rabbits and mice, following immune responses induced by various foreign antigens. AAL can specifically bind to fucose moieties on glycoproteins. However, most serum IgGs are poorly bound by AAL unless they are denatured or treated with glycosidase. In this study, using an immunogen-independent AAL-antibody microarray assay that we developed, we detected AAL-reactive IgG in the sera of all animals that had been immunized 1-2 weeks previously with various immunogens with and without adjuvants and developed immunogen-specific responses. All of these animals subsequently developed immunogen-specific immune responses. The kinetics of the production of AAL-reactive IgG in mice and rabbits were distinct from those of the immunogen-specific IgGs elicited in the same animals: they rose and fell within one to two weeks, and peaked between four to seven days after exposure, while immunogen-specific IgGs continued to rise during the same period. Mass spectrometric profiling of the Fc glycoforms of purified AAL-reactive IgGs indicates that these are mainly comprised of IgGs with core-fucosylated and either mono-or non-galactosylated Fc N-glycan structures. Our results suggest that AAL-reactive IgG could be a previously unrecognized IgG subset that is selectively produced at the onset of a humoral response.