CLIPPER: an add-on to the Trans-Proteomic Pipeline for the automated analysis of TAILS N-terminomics data

Data analysis in proteomics is complex and with the extra challenges involved in the interpretation of data from N-terminomics experiments, this can be daunting. Therefore, we have devised a rational pipeline of steps to approach N-terminomics data analysis in a statistically-based and valid manner. We have automated these steps in CLIPPER, an add-on to the Trans-Proteomic Pipeline (TPP). Applying CLIPPER to the analysis of N-terminomics data generated by terminal amine isotopic labeling of substrates (TAILS) enables high confidence peptide to protein assignment, protein N-terminal characterization and annotation, and for protease analysis readily allows protease substrate discovery with high confidenc

Factor Xa subsite mapping by proteome-derived peptide libraries improved using WebPICS, a resource for proteomic identification of cleavage sites

Proteomic identification of protease cleavage site specificity (PICS) is a recent proteomic approach for the easy mapping of protease subsite preferences that determines both the prime- and non-prime side specificity concurrently. Here we greatly facilitate user access by providing an automated and simple web-based data-analysis resource termed WebPics (http://clipserve.clip.ubc.ca/pics/). We demonstrate the utility of WebPics analysis of PICS data by determining the substrate specificity of factor Xa from P6-P6', an important blood coagulation protease that proteolytically generates thrombin from prothrombin. PICS confirms existing data on non-prime site specificity and refines our knowledge of factor Xa prime-site selectivit

TAILS N-terminomic and proteomic datasets of healthy human dental pulp

AbstractThe Data described here provide the in depth proteomic assessment of the human dental pulp proteome and N-terminome (Eckhard et al., 2015) [1]. A total of 9 human dental pulps were processed and analyzed by the positional proteomics technique TAILS (Terminal Amine Isotopic Labeling of Substrates) N-terminomics. 38 liquid chromatography tandem mass spectrometry (LC-MS/MS) datasets were collected and analyzed using four database search engines in combination with statistical downstream evaluation, to yield the by far largest proteomic and N-terminomic dataset of any dental tissue to date. The raw mass spectrometry data and the corresponding metadata have been deposited in ProteomeXchange with the PXD identifier <http://www.ebi.ac.uk/pride/archive/projects/PXD002264>; Supplementary Tables described in this article are available via Mendeley Data (10.17632/555j3kk4sw.1)

Hydrolases in GtoPdb v.2023.1

Listed in this section are hydrolases not accumulated in other parts of the Concise Guide, such as monoacylglycerol lipase and acetylcholinesterase. Pancreatic lipase is the predominant mechanism of fat digestion in the alimentary system; its inhibition is associated with decreased fat absorption. CES1 is present at lower levels in the gut than CES2 (P23141), but predominates in the liver, where it is responsible for the hydrolysis of many aliphatic, aromatic and steroid esters. Hormone-sensitive lipase is also a relatively non-selective esterase associated with steroid ester hydrolysis and triglyceride metabolism, particularly in adipose tissue. Endothelial lipase is secreted from endothelial cells and regulates circulating cholesterol in high density lipoproteins

Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini

Translation initiation generally occurs at AUG codons in eukaryotes, although it has been shown that non-AUG or non-canonical translation initiation can also occur. However, the evidence for noncanonical translation initiation sites (TISs) is largely indirect and based on ribosome profiling (Ribo-seq) studies. Here, using a strategy specifically designed to enrich N termini of proteins, we demonstrate that many human proteins are translated at noncanonical TISs. The large majority of TISs that mapped to 5' untranslated regions were noncanonical and led to N-terminal extension of annotated proteins or translation of upstream small open reading frames (uORF). It has been controversial whether the amino acid corresponding to the start codon is incorporated at the TIS or methionine is still incorporated. We found that methionine was incorporated at almost all noncanonical TISs identified in this study. Comparison of the TISs determined through mass spectrometry with ribosome profiling data revealed that about two-thirds of the novel annotations were indeed supported by the available ribosome profiling data. Sequence conservation across species and a higher abundance of noncanonical TISs than canonical ones in some cases suggests that the noncanonical TISs can have biological functions. Overall, this study provides evidence of protein translation initiation at noncanonical TISs and argues that further studies are required for elucidation of functional implications of such noncanonical translation initiation

Hydrolases (version 2019.4) in the IUPHAR/BPS Guide to Pharmacology Database

Listed in this section are hydrolases not accumulated in other parts of the Concise Guide, such as monoacylglycerol lipase and acetylcholinesterase. Pancreatic lipase is the predominant mechanism of fat digestion in the alimentary system; its inhibition is associated with decreased fat absorption. CES1 is present at lower levels in the gut than CES2 (P23141), but predominates in the liver, where it is responsible for the hydrolysis of many aliphatic, aromatic and steroid esters. Hormone-sensitive lipase is also a relatively non-selective esterase associated with steroid ester hydrolysis and triglyceride metabolism, particularly in adipose tissue. Endothelial lipase is secreted from endothelial cells and regulates circulating cholesterol in high density lipoproteins

Power Generation and Visual Comfort Performance of Photovoltaic Toplighting Technologies in Transient Spaces

Advances in long-span glazed structures and interest in high-performance building design has proliferated semi-conditioned spaces with large areas of overhead glazing. These spaces are often programmed with intermittent occupation where variability of the indoor climate is an intentional factor of the experience. Technological options for glazed canopy structures have likewise evolved, gaining functions such as power generation which diversifies the benefits of overhead glazing beyond weather protection and daylighting. Here we model the multiple benefits of current and emerging toplighting technologies deployed in the overhead glazing of a train station and compare power generation and visual comfort. A common building integrated photovoltaic system comprised of monocrystalline cells embedded in the interlayer of laminated glazing is compared with a dynamic, tracking solar collector technology that concentrates and largely intercepts direct solar energy but is transmissive to diffuse sky radiation. The concentrating system generates 6% more power annually with a 70% higher peak power production compared to a typical fixed PV system while at times significantly reducing glare

Microarray tools and analysis methods to better characterize biological networks

To accurately model a biological system (e.g. cell), we first need to characterize each of its distinct networks. While omics data has given us unprecedented insight into the structure and dynamics of these networks, the associated analysis routines are more involved and the accuracy and precision of the experimental technologies not sufficiently examined. The main focus of our research has been to develop methods and tools to better manage and interpret microarray data. How can we improve methods to store and retrieve microarray data from a relational database? What experimental and biological factors most influence our interpretation of a microarray's measurements? By accounting for these factors, can we improve the accuracy and precision of microarray measurements? It's essential to address these last two questions before using 'omics data for downstream analyses, such as inferring transciption regulatory networks from microarray data. While answers to such questions are vital to microarray research in particular, they are equally relevant to systems biology in general. We developed three studies to investigate aspects of these questions when using Affymetrix expression arrays. In the first study, we develop the Data-FATE framework to improve the handling of large scientific data sets. In the next two studies, we developed methods and tools that allow us to examine the impact of physical and technical factors known or suspected to dramatically alter the interpretation of a microarray experiment. In the second study, we develop ArrayInitiative -- a tool that simplifies the process of creating custom CDFs -- so that we can easily re-design the array specifications for Affymetrix 3' IVT expression arrays. This tool is essential for testing the impact of the various factors, and for making the framework easy to communicate and re-use. We then use ArrayInitiative in a case study to illustrate the impact of several factors known to distort microarray signals. In the third study, we systematically and exhaustively examine the effect of physical and technical factors -- both generally accepted and novel -- on our interpretation of dozens of experiments using hundreds of E. coli Affymetrix microarrays

Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines)

Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process