Conrad Bessant

Cranfield University · Department of Engineering Computing

Proteomics informed by transcriptomics (PIT), in which proteomic MS/MS spectra are searched against open reading frames derived from de novo assembled transcripts, can reveal previously unknown translated genomic elements (TGEs). However, determining which TGEs are truly novel, which are variants of known proteins, and which are simply artefacts of...

PITDB is a freely available database of translated genomic elements (TGEs) that have been observed in PIT (proteomics informed by transcriptomics) experiments. In PIT, a sample is analyzed using both RNA-seq transcriptomics and proteomic mass spectrometry. Transcripts assembled from RNA-seq reads are used to create a library of sample-specific amin...

Background Aedes aegypti is a vector for the (re-)emerging human pathogens dengue, chikungunya, yellow fever and Zika viruses. Almost half of the Ae. aegypti genome is comprised of transposable elements (TEs). Transposons have been linked to diverse cellular processes, including the establishment of viral persistence in insects, an essential step i...

Background/objectives: Enteral feeding will induce remission in as many as 80-90% of compliant patients with active Crohn's disease (CD), but its method of action remains uncertain. This study was designed to examine its effects on the colonic microbiome. Methods/subjects: Healthy volunteers and patients with CD followed a regimen confined to en...

Previous studies have indicated that volatile organic compounds specific to bladder cancer may exist in urine headspace, raising the possibility that they may be of diagnostic value for this particular cancer. To further examine this hypothesis, urine samples were collected from patients diagnosed with either bladder cancer or a non-cancerous urolo...

The developed world has seen an alarming increase in the incidence of gastrointestinal diseases, among the most common of which is Crohn's disease (CD) in the young. The current " gold standard " techniques for diagnosis are often costly, time consuming, inefficient, invasive, and offer poor sensitivities and specificities. This paper compares the...

The use of vibrational spectroscopy for diagnosis and staging of cancer is extremely attractive, promising many benefits over the currently used histopathology methods. The hypothesis underlying this approach is that cancers have characteristic biochemical fingerprints that can be captured using spectroscopy. To relate complex multivariate spectra...

The aim of this study was to determine whether volatile organic compounds (VOCs) present in the headspace of feces could be used to diagnose or distinguish between chronic diseases of the gastrointestinal tract and apparently healthy volunteers. A total of 87 people were recruited, divided between 4 categories: healthy volunteers (n = 19), Crohn's...

Selected reaction monitoring (SRM) is becoming the tool of choice for targeted quantitative proteomics, with applications as diverse as clinical diagnostics and systems biology. Assay design is critical to the success of every SRM experiment. For each protein of interest it is necessary to find a set of peptides that can be monitored as surrogates...

Selected reaction monitoring (SRM), sometimes called multiple reaction monitoring (MRM), is becoming the tool of choice for targeted quantitative proteomics in the plant science community. Key to a successful SRM experiment is prior identification of the distinct peptides for the proteins of interest and the determination of the so-called transitio...

Proteins identified from discovery Orbitrap LC-MS analysis to generate candidate protein list.

Full results from PRIDE-MRMaid predicted transitions, Orbitrap-Skyline transitions and testing of 2+ or 3+ charge states for peptides over 1000 m/z.

List of candidate proteins for testing MRMaid.

Simplified transition list manually edited from MRMaid output.

Transition list derived from Orbitrap discovery LC-MS analysis and Skyline.

MRMaid output for 25 candidate proteins.

Abstract Selected reaction monitoring (SRM) is becoming the tool of choice for targeted quantitative proteomics. The fundamental principle of proteomic SRM is that, for a given protein of interest, there is a set of peptides that are unique to that protein. The characteristic retention time (RT), and intact peptide m/z of these so-called proteotypi...

Over the past years Fourier transform infrared (FTIR) spectroscopy has been demonstrated as a prospective tool for cancer diagnostics. In order to apply FTIR spectroscopy as a routine tool for biomedical diagnostics of tissue samples, strong and reliable classifiers are needed. Frequently, the number of available tissue samples is restricted and du...

Allergen detection and quantification is an essential part of allergen management as practiced by food manufacturers. Recently, protein MS methods (in particular, multiple reaction monitoring experiments) have begun to be adopted by the allergen detection community to provide an alternative technique to ELISA and PCR methods. MS analysis of protein...

A series of partial least squares (PLS) models were employed to correlate spectral data from FTIR analysis with beef fillet spoilage during aerobic storage at different temperatures (0, 5, 10, 15, and 20 °C) using the dataset presented by Argyri et al. (2010). The performance of the PLS models was compared with a three-layer feed-forward artificial...

Over recent years, Raman spectroscopy has been demonstrated as a prospective tool for application in cancer diagnostics. The use of Raman spectroscopy for this purpose relies on pattern recognition methods that have been developed to perform well on data achieved under laboratory conditions. However, the application of Raman spectroscopy as a routi...

Drinking water attained from aquifers (ground water) is susceptible to contamination from a wide variety of sources. The importance of ensuring that the water is of high quality is paramount. Multivariate calibration in conjunction with analytical techniques can assist in qualifying and quantifying a wide range of pollutants. These can be divided i...

The optimization of DNA hybridization for genotyping assays is a complex experimental problem that depends on multiple factors such as assay formats, fluorescent probes, target sequence, experimental conditions, and data analysis. Quantum dot-doped particle bioconjugates have been previously described as fluorescent probes to identify single nucleo...

We investigated the potential of two different electronic noses (EN; code named “Rob” and “Walter”) to differentiate between sputum headspace samples from tuberculosis (TB) patients and non-TB patients. Only samples from Ziehl-Neelsen stain (ZN)- and Mycobacterium tuberculosis culture-positive (TBPOS) sputum samples and ZN- and culture-negative (TB...

Clinical drug discovery in most cases begins with molecular screening in order to select a lead-substance. This process is a key step in successful drug development. Lead-substances are marked based on their ability to affect objective biological properties. In order to judge the molecular efficacy of a lead-substance, both animal experimentation a...

Previous studies have indicated that volatile compounds specific to bladder cancer may exist in urine headspace, raising the possibility that headspace analysis could be used for diagnosis of this particular cancer. In this paper, we evaluate the use of a commercially available gas sensor array coupled with a specifically designed pattern recogniti...

This study concerns the combination of Raman spectroscopy and multivariate statistical analyses for the assessment of lymph nodes in the course of breast cancer diagnostics and staging. Axillary lymph node samples derived from breast cancer patients were measured by Raman microspectroscopy. The resulting Raman maps were pre-processed and cleaned of...

Selected reaction monitoring (SRM) is a technique for quantifying specific proteins using triple quadrupole MS. Proteins are digested into peptides and fed into MS following HPLC separation. The stream of ionized peptides is filtered by m/z ratio so only specific peptide targets enter the collision cell, where they are fragmented into product ions....

Multiple reaction monitoring (MRM) of peptides is a popular proteomics technique that employs tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential protein identification studies. Using this technique, the specificity of precursor to product transitions is exploited to determine the...

Selected reaction monitoring (SRM) is a technique that applies tandem mass spectrometry to quantify specific proteins of biological interest. The key to SRM is finding the best peptide-to-product ion transitions to monitor. The MRMaid database (MRMaid-DB) is a new online database for capturing SRM transitions from published research papers to save...

The currently accepted 'gold standard' tuberculosis (TB) detection method for veterinary applications is that of culturing from a tissue sample post mortem. The test is accurate, but growing Mycobacterium bovis is difficult and the process can take up to 12 weeks to return a diagnosis. In this paper we evaluate a much faster screening approach base...

A workflow based on the Taverna Workbench® software and tentatively named WPSA was developed to perform a generic protein sequence analysis eliminating the need to cut and paste data throughout web applications. The program performs a homology search, a multiple sequence alignment and a phylogeny analysis using PHYLogeny Interface Package (PHYLIP)....

This paper presents Fourier transform infrared (FT-IR) spectroscopy to characterise spectral differences that distinguish cells derived from human T-cell lymphoma, B-cell lymphoid, and myeloid leukaemia cell lines. This methodology is based on spectral measurements of major cellular biochemical constituents and multivariate spectral processing. Maj...

Decoy database searches are routinely applied as a null model to determine threshold scores for filtering protein identifications reported by search engines such as Mascot. Various methods have been published for generating decoy databases, but there is debate about which decoy is “the best”. This paper addresses this question by performing an eval...

A combination of selective fluorescent dyes has been developed for simultaneous quantitative measurements of several physicochemical parameters. The operating principle of the assay is similar to electronic nose and tongue systems, which combine nonspecific or semispecific elements for the determination of diverse analytes and chemometric technique...

This article provides an overview of publicly available proteomic data repositories in a single document with a particular focus on the latest developments, many of which are not announced through traditional publications. The review is intended to inform the proteomics practitioner of the options for storage and dissemination of their MS/MS data i...

Water is a vital commodity for every living entity on the planet. However, water resources are threatened by various sources of contamination from pesticides, hydrocarbons and heavy metals. This has resulted in the development of concepts and technologies to create a basis for provision of safe and high quality drinking water. This paper focuses on...

Multiple reaction monitoring (MRM) of peptides uses tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential studies. Using this technique, the specificity of precursor to product transitions is harnessed for quantitative analysis of multiple proteins in a single sample. The design of t...

Metals are needed by at least one-quarter of all proteins. Although metallochaperones insert the correct metal into some proteins, they have not been found for the vast majority, and the view is that most metalloproteins acquire their metals directly from cellular pools. However, some metals form more stable complexes with proteins than do others....

Ultrasound scanning uses the medical imaging format, DICOM, for electronically storing the images and data associated with a particular scan. Large health care facilities typically use a picture archiving and communication system (PACS) for storing and retrieving such images. However, these systems are usually not suitable for managing large collec...

As proteomic MS has increased in throughput, so has the demand to catalogue the increasing number of peptides and proteins observed by the community using this technique. As in other 'omics' fields, this brings obvious scientific benefits such as sharing of results and prevention of unnecessary repetition, but also provides technical insights, such...

This paper presents a novel method to characterise spectral differences that distinguish leukaemia and lymphoma cell lines. This is based on objective spectral measurements of major cellular biochemical constituents and multivariate spectral processing. Fourier transform infrared (FT-IR) maps of the lymphoma, lymphoid and myeloid leukaemia cell sam...

A gene regulatory network (GRN) extracted from microarray data has the potential to give us a concise and precise way of understanding how genes interact under the experimental conditions studied [1, 2]. Learning such networks, and unravelling the knowledge hidden within them is important for drug targets and to understand the basis of disease. In...

Proteomics based on tandem mass spectrometry is a powerful tool for identifying novel biomarkers and drug targets. Previously, a major bottleneck in high-throughput proteomics has been that the computational techniques needed to reliably identify proteins from proteomic data lagged behind the ability to collect the immense quantity of data generate...

This paper introduces the genome annotating proteomic pipeline (GAPP), a totally automated publicly available software pipeline for the identification of peptides and proteins from human proteomic tandem mass spectrometry data. The pipeline takes as its input a series of MS/MS peak lists from a given experimental sample and produces a series of dat...

Ziehl-Neelsen (ZN) staining for the diagnosis of tuberculosis (TB) is time-consuming and operator dependent and lacks sensitivity. A new method is urgently needed. We investigated the potential of an electronic nose (EN) (gas sensor array) comprising 14 conducting polymers to detect different Mycobacterium spp. and Pseudomonas aeruginosa in the hea...

Microarray technology for mammalian cells has been utilized mainly for humans, mouse, and rat gene expression analysis. In this approach the feasibility of cross-species hybridization experiments using Chinese hamster ovary (CHO) cells was evaluated. Sequence alignments of available data for CHO were performed against mouse and rat transcripts to d...

A challenging task in the study of the secretory pathway is the identification and localization of new proteins to increase our understanding of the functions of different organelles. Previous proteomic studies of the endomembrane system have been hindered by contaminating proteins, making it impossible to assign proteins to organelles. Here we hav...

As proteins within cells are spatially organized according to their role, knowledge about protein localization gives insight into protein function. Here, we describe the LOPIT technique (localization of organelle proteins by isotope tagging) developed for the simultaneous and confident determination of the steady-state distribution of hundreds of i...

Perhaps the greatest difficulty in interpreting large sets of protein identifications derived from mass spectrometric methods is whether or not to trust the results. For such experiments, the level of confidence in each protein identification made needs to be far greater than the often used 95% significance threshold to avoid the identification of...

Current proteomics experiments can generate vast quantities of data very quickly, but this has not been matched by data analysis capabilities. Although there have been a number of recent reviews covering various aspects of peptide and protein identification methods using MS, comparisons of which methods are either the most appropriate for, or the m...

We demonstrate a new approach to the determination of amino acid composition from tandem mass spectrometrically fragmented peptides using both experimental and simulated data. The approach has been developed to be used as a search-space filter in a protein identification pipeline with the aim of increased performance above that which could be attai...

iTRAQ technology for protein quantitation using mass spectrometry is a recent, powerful means of determining relative protein levels in up to four samples simultaneously. Although protein identification of samples generated using iTRAQ may be carried out using any current identification software, the quantitation calculations have been restricted t...

An ever-increasing number of patients have to undergo regular renal dialysis to compensate for acute or chronic renal failure. The adequacy of the treatment has a profound effect on patients' morbidity and mortality. Therefore, it is necessary to assess the delivered dialysis dose. For the quantification of the dialysis dose, two parameters are mos...

This paper describes the simultaneous quantification of four aliphatic compounds (ethanol, methanol, fructose and glucose) mixed in varying concentrations. The method used employs dual pulse staircase voltammetry (DPSV) to acquire an electrochemical voltammogram from the mixture. An artificial neural network, optimised using an elitist genetic algo...

Peptide mass fingerprinting and database searching with tandem mass spectrometry are two methods commonly employed to identify proteins in a sample. However, up to 90% of peptides can remain unidentified. In this paper, a search-space filter using amino acids identified by a novel de nova methodology is presented. This provides a high-accuracy set...

Drug discovery (DD) research has evolved to the point of critical dependence on computerized systems, databases and newer disciplines. Such disciplines include but are not limited to bioinformatics, chemoinformatics and soft computing. Their applications range from sequence analysis methods for finding biological targets to design of combinatorial...

In a recent publication we introduced a novel method for detection of impurities on beverage can surfaces using Raman spectroscopy. While investigating the technique, limitations emerged due to the low sensitivity of Raman scatter. This is a particular problem with the largest contributor of impurities in beverage cans: lubricants employed in the m...

Multivariate calibration of a single sensor for many mixed analytes is useful, but generating, validating and testing the calibration models requires large data sets which can be time consuming to collect, particularly when the number of analytes is large. In this paper, a solution to this problem is presented, in the form of an automated liquid ha...

Data analysis is becoming an increasingly important aspect of electroanalytical chemistry, as voltammetric techniques and electrode arrays become ever more popular as diagnostic tools. Modern data analysis techniques promise to help us make full use of the large amounts of data collected, allowing electroanalytical chemists to get more out of their...

Raman microspectroscopy is ideally suited to surface analysis as it allows detailed chemical information to be acquired from surfaces at a relatively high spatial resolution (typically 1 µm). Using a motorised sample table or probe, it is possible to raster scan a surface to obtain spatially resolved chemical information. Visualisation of the acqui...

Neural networks are powerful tools for the calibration of multivariate analytical data, but the large number of network parameters make it difficult to obtain an optimum calibration model. Often, network parameters are guessed or chosen according to postulated ‘rules of thumb.’ In this paper, we perform a thorough network optimisation for the calib...

Impurities in beverage can production cause serious quality problems. In this paper, an alternative method to the analytical techniques currently used to characterise such impurities is suggested and tested. Rather than relying on conductivity measurements or visual tests, a spectroscopic approach using Raman microprobe equipment has been chosen. T...

This paper describes the evaluation of synchronous scan fluorescence spectroscopy as a means of determining key characteristics of mineral insulating oils that are used in electrical apparatus around the world. Characteristics of interest to commercial operators include regulatory conformance, the history of the oil (whether it has been used or not...

In a previous paper we reported that by using artificial neural networks (ANNs) to interpret data acquired using dual pulse staircase voltammetry (DPSV), it is possible to determine the concentrations of aliphatic compounds in mixtures. This paper extends that work by probing the relationship between the DPSV response and mixture composition by fit...

Dual pulse staircase voltammetry (DPSV)a combination of pulsed electrochemical detection and staircase voltammetryis investigated for the simultaneous determination of glucose, fructose, and ethanol in mixtures. Each analyte is found to elicit a distinctive response at a platinum electrode in an alkaline solution. A method is devised for visualizin...

This work describes the application of object oriented software design to the development of a low cost, functionally versatile, PC-controlled potentiostat system. The implementation time for the electroanalytical techniques has been drastically reduced within the object oriented environment and it is shown how this approach simplifies the addition...