Alisa G Woods

Clarkson University · Department of Chemistry & Biomolecular Science

Of the 25,000–30,000 human genes, about 2 % code for proteins. However, there are about 1-2 million protein entities. This is primarily due to alternative splicing, post-translational modifications (PTMs) or protein-protein interactions. Proteomics sets out to identify proteins, their sequence and known modifications as well as their quantitation i...

Better understanding of central nervous system (CNS) molecules can include the identification of new molecules and their receptor systems. Discovery of novel proteins and elucidation of receptor targets can be accomplished using mass spectrometry (MS). We describe a case study of such a molecule, which our lab has studied using MS in combination wi...

Major depressive disorder (MDD) is common. Despite numerous available treatments, many individuals fail to improve clinically. Diagnosis of MDD continues to be commonly accomplished via behavioral rather than biological methods. Biomarkers may provide objective diagnosis of MDD, and could include measurements of genes, proteins, and patterns of bra...

Within the past years, we have witnessed a great improvement is mass spectrometry (MS) and proteomics approaches in terms of instrumentation, protein fractionation, and bioinformatics. With the current technology, protein identification alone is no longer sufficient. Both scientists and clinicians want not only to identify the proteins, but also to...

Mass spectrometry (MS) has been increasingly used to study central nervous system (CNS) disorders, including autism spectrum disorders (ASDs). The first studies of ASD using MS focused on the identification of external toxins, but current research is more directed at understanding endogenous protein changes that occur in ASD (ASD proteomics). This...

There are only 30,000 human genes, which, according to the central dogma from biology, it means that there should be 30,000 mRNA and 30,000 proteins. However, there are at least 1-2 million protein entities that are expressed in a cell at a given time. This is primarily due to alternative splicing in different cells and tissues, which may lead to e...

Recent developments of mass spectrometry (MS) allow us to identify, estimate, and characterize proteins and protein complexes. At the same time, structural biology helps to determine the protein structure and its structure-function relationship. Together, they aid to understand the protein structure, property, function, protein-complex assembly, pr...

The chapter “2D SDS PAGE in Combination with Western Blotting and Mass Spectrometry Is a Robust Method for Protein Analysis with Many Applications” is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com.

“Mind-body medicine” is frequently used to describe the balancing effects between mind and body of nonpharmacological behavioral interventions applied to stress-related psychiatric disorders—including MDD. Recent studies find powerful biological changes associated with mind-body interventions comparable to those associated with conventional antidep...

Table S1 Summary results for 2D gel comparison of saliva samples.

Figure S1 The Mascot MS/MS spectra and their corresponding MS/MS spectra from the original raw data (.raw).

Current directions in autism spectrum disorder (ASD) research may require moving beyond genetic analysis alone, based on the complexity of the disorder, heterogeneity and convergence of genetic alterations at the cellular/functional level. Mass spectrometry (MS) has been increasingly used to study central nervous system (CNS) disorders, including A...

Biomarkers are greatly needed in the fields of neurology and psychiatry, to provide objective and earlier diagnoses of CNS conditions. Proteomics and other omic mass-spectrometry-based technologies are tools currently being utilized in much recent CNS research. Saliva is an interesting alternative biomaterial for the proteomic study of CNS disorder...

Autism spectrum disorder (ASD) prevalence is increasing, with current estimates at 1/68–1/50 individuals diagnosed with an ASD. Diagnosis is based on behavioral assessments. Early diagnosis and intervention is known to greatly improve functional outcomes in people with ASD. Diagnosis, treatment monitoring and prognosis of ASD symptoms could be faci...

In the last decades, prevalence of autism spectrum disorder (ASD) has been on the rise. However, clear aetiology is still elusive and improvements in early diagnosis are needed. To uncover possible biomarkers present in ASD, we used two-dimensional polyacrylamide gel electrophoresis and nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/...

Age may bring wisdom—but it frequently comes with cognitive decline. This can be mild, due to normal aging, or severe, as in Alzheimer disease. Research is increasingly important as life expectancy increases. Aging has numerous brain effects, including decreases in many processes that contribute to plasticity. Three simultaneously published reports...

Mass spectrometry is the central tool used in proteomic research today and is rapidly becoming indispensable to the biomedical scientist. With the completion of the human genome project and the genomic revolution, the proteomic revolution has followed closely behind. Understanding the human proteome has become critical to basic and clinical biomedi...

Autism spectrum disorder (ASD) diagnosis is increasing, with 1/88 children believed to be affected by the disorder, with a most recent survey suggesting numbers as high as 1/50. Treatment and understanding of ASD causes is a pressing health concern. ASD protein biomarkers may provide clues about ASD cause. Protein biomarkers for ASDs could be used...

Of the 25,000-30,000 human genes, about 2 % code for proteins. However, there are about one to two million protein entities. This is primarily due to alternative splicing and post-translational modifications (PTMs). Identifying all these modifications in one proteome at a particular time point during development or during the transition from normal...

Better understanding of central nervous system (CNS) molecules can include the identification of new molecules and their receptor systems. Discovery of novel proteins and elucidation of receptor targets can be accomplished using mass spectrometry (MS). We describe a case study of such a molecule, which our lab has studied using MS in combination wi...

Major depressive disorder (MDD) is common. Despite numerous available treatments, many individuals fail to improve clinically. MDD continues to be diagnosed exclusively via behavioral rather than biological methods. Biomarkers-which include measurements of genes, proteins, and patterns of brain activity-may provide an important objective tool for t...

Mass spectrometry (MS) has been increasingly used to study central nervous system disorders, including autism spectrum disorders (ASDs). The first studies of ASD using MS focused on the identification of external toxins, but current research is more directed at understanding endogenous protein changes that occur in ASD (ASD proteomics). This chapte...

Within the past years, we have witnessed a great improvement in mass spectrometry (MS) and proteomics approaches in terms of instrumentation, protein fractionation, and bioinformatics. With the current technology, protein identification alone is no longer sufficient. Both scientists and clinicians want not only to identify proteins but also to iden...

Recent developments of mass spectrometry (MS) allow us to identify, estimate, and characterize proteins and protein complexes. At the same time, structural biology helps to determine the protein structure and its structure-function relationship. Together, they aid to understand the protein structure, property, function, protein-complex assembly, pr...

It’s hard to believe that 40 years ago it was proposed that Alzheimer disease (AD) is caused by brain aluminum. Some people even threw out their cookware, in fear of acquiring the memory-impairing disease. The aluminum hypothesis has long since been discounted, and research has marched forward: β-amyloid (Aβ) protein was identified in 1984 in brain...

Tumor Differentiation Factor (TDF) is a pituitary protein, which is secreted into the blood stream and targets breast and prostate. The end effect of TDF on these tissues is differentiation of breast and prostate cells. However, it is not yet clear how TDF induces cell differentiation. Studies in our laboratory determined that the potential TDF rec...

Autism Spectrum Disorder (ASD) diagnosis is increasing with approximately 1/68 children in the United States diagnosed with an ASD [1]. A recent survey of parents indicated that this number may be as high as 1/50 [2]. ASDs are approximately 4.5 times more prevalent in boys than girls [3]. ASDs are characterized by impaired social interactions, comm...

The etiology and pathogenesis of many psychiatric disorders are unclear with many signaling pathways and complex interactions still unknown. Primary information provided from gene expression or brain activity imaging experiments is useful, but can have limitations. There is a current effort focusing on the discovery of diagnostic and prognostic pro...

Tumor differentiation factor (TDF) is a protein produced by the pituitary and secreted into the blood stream. The mechanism of its action has still not been elucidated, although the associated protein receptor was identified. Furthermore, the TDF protein does not have any homology with other known proteins, and the crystal structure of TDF also is...

Asperger's syndrome (AS) is a form of autism spectrum disorder (ASD) affecting many individuals today. Although neurobiological correlates for AS have been identified, like many ASDs, AS is not completely understood. AS as a distinct disorder is also not universally accepted and in the DSM-5 AS is not considered a separate nosological entity. In co...

Tumor Differentiation Factor (TDF) is a protein produced by the pituitary and secreted into the blood stream. TDF targets breast and prostate and induces cell differentiation. However, the mechanism of cell differentiation, the TDF receptor and the TDF pathway have not been adequately investigated. Here, we provide some insights about the possible...

Autism Spectrum Disorder (ASD) diagnosis is increasing worldwide. ASDs are characterized by impaired social function, stereotyped behaviors/interests and communication deficits. ASD causes are poorly understood and treatments are largely limited to behavioral interventions once problems have developed and been detected. Here we discuss the potentia...

Hepatitis B virus (HBV) is a human pathogen causing severe liver disease and eventually death. Despite important progress in deciphering HBV internalization, the early virus-cell interactions leading to infection are not known. HepaRG is a human bipotent liver cell line bearing the unique ability to differentiate towards a mixture of hepatocyte- an...

Total protein profile of PM isolated from (ND) and (D) HepaRG cells. PM fractions were purified from an equal number of (ND) and (D) HepaRG cells. The proteins were extracted and analyzed by SDS-PAGE followed by Coomassie staining (A), or further transferred onto PVDF membrane and stained by Ponceau S (B). The molecular weight markers are indicated...

HBV infection in the presence of Cathepsin D inhibitors. (D) HepaRG cells were treated with Pepstatin A for 24 h either during HBV infection (2) or following removal of the viral inoculum (3). HBV transcripts was quantified by RT-real time PCR at day 14 post-viral inoculation and the results were expressed as percentage from untreated cells (1). Th...

Proteins with a role in viral reproduction. This classification resulted from the analysis of the Mascot results shown in Tables S1 and S2, using the Scaffold software-version 4.0.4. (DOCX)

MS/MS spectra of proteins identified by one peptide (I). The proteins were found in PM of (ND) cells, in experiment 1 (Mascot scores higher than 25). (PDF)

Analysis of differentially expressed proteins at PMs of (D) naïve and HBV-infected HepaRG cells. The PM fractions of (D) cells infected (+) or not (−) with HBV were analyzed by Western blotting using Annexin A1- and PDI-specific Abs. The molecular weight markers are indicated. (TIF)

MS/MS spectra of proteins identified by one peptide (II). The proteins were found in PM of (D) cells, in experiment 1 (Mascot scores higher than 25). (PDF)

Relative quantification of Annexins. The number of spectra identified for Annexins A1, A2, A4 and A5 in (ND) and (D) HepaRG cells, in experiments 1 and 2 (A). Direct comparison of the precursor ions corresponding to peptides derived from Annexins (B). Precursor ion 851.92 (2+) and peptide GLGTDEDTLIEILASR, derived from Annexin A1; precursor ion 615...

Summary of the LC/MS/MS analysis showing the proteins identified at the PM of (ND) and (D) cells (experiment 1). (XLS)

Summary of the LC/MS/MS analysis showing the proteins identified at the PM of (ND) and (D) cells (experiment 2). (XLS)

Proteins are the effector molecules of many cellular and biological processes and are thus very dynamic and flexible. Regulation of protein activity, structure, stability, and turnover is in part controlled by their post-translational modifications (PTMs). Common PTMs of proteins include phosphorylation, glycosylation, methylation, ubiquitination,...

Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands o...

The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identificatio...

Identification of central nervous system (CNS) molecules elucidates normal and pathological brain function. Tumor differentiation factor (TDF) is a recently-found protein secreted by the pituitary into the blood. TDF mRNA was detected in brain; not heart, placenta, lung, liver, skeletal muscle, or pancreas. However, TDF has an unclear function. It...

The search for molecules that can act as potential biomarkers is increasing in the scientific community, including in the field of psychiatry. The field of proteomics is evolving and its indispensability for identifying biomarkers is clear. Among proteomic tools, mass spectrometry is the core technique for qualitative and quantitative identificatio...

Autism spectrum disorders (ASDs) are increasing in incidence but have an incompletely understood etiology. Tools for uncovering clues to the cause of ASDs and means for diagnoses are valuable to the field. Mass Spectrometry (MS) has been a useful method for evaluating differences between individuals with ASDs versus matched controls. Different biol...

Following the sequencing of the human genome and many other organisms, research on protein-coding genes and their functions (functional genomics) has intensified. Subsequently, with the observation that proteins are indeed the molecular effectors of most cellular processes, the discipline of proteomics was born. Clearly, proteins do not function as...

This article presents an overview of the literature and a review of recent advances in the analysis of stable and transient protein–protein interactions (PPIs) with a focus on their function within cells, organs, and organisms. The significance of PTMs within the PPIs is also discussed. We focus on methods to study PPIs and methods of detecting PPI...

The field of proteomics and use of mass spectrometry as well as other proteomic techniques is continually growing, based on the interest of researchers for searching for potential biomarkers for numerous diseases and disorders. Currently protein biomarkers are not standardly used in clinical practice for diagnosing and monitoring neurodevelopmental...

Tumor differentiation factor (TDF) is a 17 kDa protein produced by the pituitary and secreted into the bloodstream, with no definitive function and incomplete characterization. TDF has the following four cysteine (Cys) residues: Cys17, Cys70, Cys97, and Cys98. To understand the function of TDF, we (1) overexpressed and characterized recombinant TDF...

Tumor differentiation factor (TDF) is an under-investigated protein produced by the pituitary with no definitive function. TDF is secreted into the bloodstream and targets the breast and prostate, suggesting that it has an endocrine function. Initially, TDF was indirectly discovered based on the differentiation effect of alkaline pituitary extracts...

Background In childhood, attention deficit/hyperactivity disorder (ADHD) is characterized by age-inappropriate levels of inattentiveness/disorganization, hyperactivity/impulsiveness, or a combination thereof. Although the criteria for ADHD are well defined, the long-term consequences in adults and children need to be more comprehensively understood...

Precise determination of disulfide linkages between cysteine (Cys) residues in proteins is essential in the determination of protein structure. Therefore, a reliable automated method for the identification of disulfide bridges can serve as an important tool in the analysis of the tertiary structure of proteins of interest. Here, we describe the cur...

Liver infection with hepatitis B virus (HBV), a DNA virus of the Hepadnaviridae family, leads to severe disease, such as fibrosis, cirrhosis and hepatocellular carcinoma. The early steps of the viral life cycle are largely obscure and the host cell plasma membrane receptors are not known. HepaRG is the only proliferating cell line supporting HBV in...

Table S1. LC/MS/MS experiment (experiment #1) of the proteins from the plasma membranes of undifferentiated (−) and differentiated (+) cells.

Figure S1. MS/MS spectra that led to identification of a protein by a unique peptide. In the (+) cells, the MS/MS spectra were identified with a Mascot score of 50 or higher. In the (−) cells, all MS/MS spectra are shown.

Table S2. LC/MS/MS experiment (experiment #2) of the proteins from the plasma membranes of undifferentiated (−) and differentiated (+) cells.

The secretome represents the set of proteins secreted into the extracellular space of cells. These proteins have been shown to play a major role in cell-cell communication. For example, recent observations revealed the presence of diffusible factors with proliferative properties in the secretome of cancer cells. Thus, a qualitative and quantitative...

Tumor differentiation factor (TDF) is a pituitary protein that is secreted into the bloodstream and has an endocrine function. TDF and TDF-P1, a 20-residue peptide selected from the ORF of TDF, induce differentiation in human breast and prostate cancer cells, but not in other cells. TDF has no known mechanism of action. In our recent study, we iden...

Blue Native polyacrylamide gel electrophoresis (BN-PAGE) is a relatively new method that separates protein complexes under native conditions, due to the external charge induced by Coomassie dye and according to their molecular weight (Mw). Colorless Native PAGE is a method similar to BN-PAGE, except that Coomassie dye is not used and therefore, sep...

Measuring biomarkers to identify and assess illness is a strategy growing in popularity and relevance. Although already in clinical use for treating and predicting cancer, no biological measurement is used clinically for any psychiatric disorder. Biomarkers could predict the course of a medical problem, and aid in determining how and when to treat....

There is increased global recognition of attention deficit hyperactivity disorder (ADHD) as a serious medical condition with long-term consequences. Although originally conceived of as a childhood disorder, ADHD is being increasingly recognized in adults. Individual geographic regions may have specific interests and objectives for the study of ADHD...

Introduction As awareness of ADHD has increased worldwide, interest has grown beyond the constellation of ADHD symptoms, to include long-term impact on people's lives and society in general. Objectives Examine the results of studies of long-term life consequences of ADHD. Aims To identify areas of life affected long-term by ADHD and differences i...

Introduction As awareness of ADHD has increased throughout the world, interest has grown beyond the constellation of ADHD symptoms, including long-term effects and impact on people's lives. Objectives To examine the consequences of childhood ADHD and the relevance of these outcomes in different world regions. Aims This analysis examined the publi...

Tumor differentiation factor (TDF) is a recently discovered protein, produced by the pituitary gland and secreted into the bloodstream. TDF and TDF-P1, a 20-amino acid peptide selected from the open reading frame of TDF, induce differentiation in human breast and prostate cancer cells but not in other cells. TDF protein has no identified site of ac...