Assessing the Potential of Untargeted SWATH Mass Spectrometry-Based Metabolomics to Differentiate Closely Related Exposures in Observational Studies

Mass spectrometry (MS) is increasingly used in clinical studies to obtain molecular evidence of chemical exposures, such as tobacco smoke, alcohol, and drugs. This evidence can help verify clinical data retrieved through anamnesis or questionnaires and may provide insights into unreported exposures, for example those classified as the same despite small but possibly relevant chemical differences or due to contaminants in reported exposure compounds. Here, we aimed to explore the potential of untargeted SWATH metabolomics to differentiate such closely related exposures. This data-independent acquisition MS-based profiling technique was applied to urine samples of 316 liver and 570 kidney transplant recipients from the TransplantLines Biobank and Cohort Study (NCT03272841), where we focused on the immunosuppressive drug mycophenolate, which is either supplied as a morpholino-ester prodrug or as an enteric-coated product, the illicit drug cocaine, which is usually supplied as an adulterated product, and the proton pump inhibitors omeprazole and esomeprazole. Based on these examples, we found that untargeted SWATH metabolomics has considerable potential to identify different (unreported) exposure or co-exposure metabolites and may determine variations in their abundances. We also found that these signals alone may sometimes be unable to distinguish closely related exposures, and enhancement of differentiation, for example by integration with pharmacogenomics data, is needed.

Controlled Formation of Protonated and Radical Cation Precursor Ions by Atmospheric Pressure Photoionization with μLC-MS Enables Electron Ionization and MS/MS Library Search

Atmospheric pressure photoionization (APPI) was developed as an alternative to electrospray ionization (ESI) for the generation of protonated molecules using liquid chromatography and optimized using dopants such as toluene, which predominantly forms protonated molecules, and chlorobenzene, which favors the formation of radical cations, although the latter has not been fully exploited. Based on 40 diverse low-molecular-weight compounds and micro liquid chromatography (μLC) coupled with APPI tandem mass spectrometry (APPI-MS/MS), the potential of radical cations was investigated. Chromatographic and ionization conditions were decoupled by post-column addition of methanol, allowing separate study and optimization. Due to the mass flow sensitive behavior of APPI, sensitivity is not affected by post-column dilution, and for 8 of 35 analytes, the radical cation response with μLC-APPI is better than for protonated molecules using μLC-ESI. Collision-induced fragmentation (CID) of radical cations produced within a collision energy range from 10-115 eV have, in the median, 65% of the fragments found in electron ionization (EI) spectra. This similarity allowed identification of 86% of the analytes using data-dependent acquisition (DDA) of radical cations and NIST EI library searches. We propose a workflow that uses multimodal DDA of protonated precursor molecules using ESI or APPI with toluene as a dopant, and radical cations produced by chlorobenzene-assisted μLC-APPI with post-column addition of methanol. This increases the confidence of molecular identification by allowing orthogonal library searches using MS/MS libraries for protonated precursor CID spectra and EI libraries for radical cation CID spectra.

The Origin and Implications of Artifact Ions in Bioanalytical LC–MS

Liquid chromatography–mass spectrometry (LC–MS) with electrospray ionization (ESI) is a widely used bioanalytical technique with both qualitative and quantitative applications. Ions are created by electrically charging a stream of droplets from the LC system, which evaporate and leave ions that are transferred to the mass spectrometer. Ideally, these are only from the analyte, but background ions, such as metals, impurities and coeluted species, can react with analytes producing adducts, such as [M + Na]+, [M + K]+, and multimers (2M + H+, 3M + H+, and so forth). Although well known, the extent of adduct ion formation and the implications for quantitative analysis and analyte characterization by tandem MS (MS/MS) are not fully appreciated. We summarize the problem and identify areas that should be considered when developing or using electrospray LC–MS.

652 Fate of The Contralateral Limb Following Major Lower Limb Amputation in Patients with Peripheral Arterial Disease And/Or Diabetes: Case Series from Two Regional Vascular Centres

Introduction

This is the first clinical case series to report time to ulceration, minor and major amputation of the contralateral limb (CLL) in the first 12 months following major lower limb amputation (LLA) in patients with peripheral arterial disease (PAD) and/or diabetes.

Method

Consecutive patient samples at two regional UK vascular centres were included; from 2010 to 2017 (site 1) and 2014 to 2016 (site 2). Data were extracted from electronic records for 12 months following index major LLA. Survival analyses are presented for the event of mortality in the total study population, plus major amputation-free survival, and complication-free survival in site 1 only; results are stratified by diabetes status.

Results

Of 381 patients reviewed (n = 197 site 1; n = 184 site 2), 208 (54.6%) were diagnosed with diabetes at the time of their index major LLA. The mean survival time of patients was lower in those without diabetes (HR: 0.64 [95% CI, 0.43 to 0.95], p=.03). The mean time to major amputation of the CLL or death in patients was lower in those without diabetes (HR: 0.65 [95% CI, 224 0.40 to 1.06]; p=.08). The median time to any complication of the CLL or death was greater in those without diabetes (HR: 1.25 [95% CI, 227 0.88 to 1.78]; p=.21).

Conclusions

Death rates were higher in patients without diabetes, whilst those with diabetes had high levels of CLL complications. Optimisation of care to protect the CLL following major LLA and guidance for carers, patients, and clinicians is required.

Metabolomics data complemented drug use information in epidemiological databases: pilot study of potential kidney donors

OBJECTIVE

The objective of this study was to investigate whether clinical metabolomics, which is increasingly applied in population-based and epidemiological studies, can be used to provide analytical evidence of exposures, and whether such information can be useful to strengthen and/or complement corresponding clinical database entries, taking drug use as an example.

STUDY DESIGN AND SETTING

Liquid chromatography-mass spectrometry (LC-MS) metabolomics analyses were performed on urine from 100 randomly-selected control subjects (50% females) from the TransplantLines Food and Nutrition Biobank and Cohort Study (NCT identifier 'NCT02811835'), and drugs were identified through spectral library searching and targeted signal extraction.

RESULTS

In 83 subjects for whom drug use information was available, 22 expected and 26 unexpected prescription-only drugs were identified, while 28 expected prescription-only drugs remained undetected. In addition, 7 prescription-only drugs were found in 17 subjects for whom drug use information was unavailable, and 58 over-the-counter drugs were identified in all 100 subjects.

CONCLUSION

Molecular evidence for many drugs could be retrieved from LC-MS metabolomics data, which could be useful to complement and strengthen epidemiological databases given that considerable discrepancies were found between analytically-identified drugs and drugs listed in the available clinical database.

Adduct annotation in liquid chromatography/high-resolution mass spectrometry to enhance compound identification

Annotation and interpretation of full scan electrospray mass spectra of metabolites is complicated by the presence of a wide variety of ions. Not only protonated, deprotonated, and neutral loss ions but also sodium, potassium, and ammonium adducts as well as oligomers are frequently observed. This diversity challenges automatic annotation and is often poorly addressed by current annotation tools. In many cases, annotation is integrated in metabolomics workflows and is based on specific chromatographic peak-picking tools. We introduce mzAdan, a nonchromatography-based multipurpose standalone application that was developed for the annotation and exploration of convolved high-resolution ESI-MS spectra. The tool annotates single or multiple accurate mass spectra using a customizable adduct annotation list and outputs a list of [M+H]⁺ candidates. MzAdan was first tested with a collection of 408 analytes acquired with flow injection analysis. This resulted in 402 correct [M+H]⁺ identifications and, with combinations of sodium, ammonium, and potassium adducts and water and ammonia losses within a tolerance of 10 mmu, explained close to 50% of the total ion current. False positives were monitored with mass accuracy and bias as well as chromatographic behavior which led to the identification of adducts with calcium instead of the expected potassium. MzAdan was then integrated in a workflow with XCMS for the untargeted LC-MS data analysis of a 52 metabolite standard mix and a human urine sample. The results were benchmarked against three other annotation tools, CAMERA, findMAIN, and CliqueMS: findMAIN and mzAdan consistently produced higher numbers of [M+H]⁺ candidates compared with CliqueMS and CAMERA, especially with co-eluting metabolites. Detection of low-intensity ions and correct grouping were found to be essential for annotation performance.

SWATH-MS for metabolomics and lipidomics: critical aspects of qualitative and quantitative analysis

INTRODUCTION

While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for omics, the number of target analytes is limited, must be predefined and specific methods developed. Data independent acquisition (DIA), including SWATH using quadrupole time of flight or orbitrap mass spectrometers and generic acquisition methods, has emerged as a powerful alternative technique for quantitative and qualitative analyses since it can cover a wide range of analytes without predefinition.

OBJECTIVES

Here we review the current state of DIA, SWATH-MS and highlight novel acquisition strategies for metabolomics and lipidomics and opportunities for data analysis tools.

METHOD

Different databases were searched for papers that report developments and applications of DIA and in particular SWATH-MS in metabolomics and lipidomics.

RESULTS

DIA methods generate digital sample records that can be mined retrospectively as further knowledge is gained and, with standardized acquisition schemes, used in multiple studies. The different chemical spaces of metabolites and lipids require different specificities, hence different acquisition and data processing approaches must be considered for their analysis.

CONCLUSIONS

Although the hardware and acquisition modes are well defined for SWATH-MS, a major challenge for routine use remains the lack of appropriate software tools capable of handling large datasets and large numbers of analytes.

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition

High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H]⁺ and 483 in negative mode [M-H]^-. MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously were reported in HMDB to be found in plasma. Graphical abstract Library generation workflow for LC-SWATH MS, using collision energy spread, accurate mass, and fragment annotation.

Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins

We present a comprehensive workflow for large scale (>1000 transitions/run) label-free LC-MRM proteome assays. Innovations include automated MRM transition selection, intelligent retention time scheduling that improves S/N by twofold, and automatic peak modeling. Improvements to data analysis include a novel Q/C metric, normalized group area ratio, MLR normalization, weighted regression analysis, and data dissemination through the Yale protein expression database. As a proof of principle we developed a robust 90 min LC-MRM assay for mouse/rat postsynaptic density fractions which resulted in the routine quantification of 337 peptides from 112 proteins based on 15 observations per protein. Parallel analyses with stable isotope dilution peptide standards (SIS), demonstrate very high correlation in retention time (1.0) and protein fold change (0.94) between the label-free and SIS analyses. Overall, our method achieved a technical CV of 11.4% with >97.5% of the 1697 transitions being quantified without user intervention, resulting in a highly efficient, robust, and single injection LC-MRM assay.

Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition

Characterizing changes in protein-protein interactions associated with sequence variants (e.g. disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies where cost and time are major considerations. To this end, we have coupled AP to data-independent mass spectrometric acquisition (SWATH), and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. Here, we use AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes, and propose a scalable pipeline for systems biology studies.

Interpretation of pediatric lung function: impact of ethnicity

RATIONALE

To evaluate the appropriateness of spirometric and plethysmographic reference equations in healthy young children according to ethnic origin.

METHODS

Spirometry data were collated in 400 healthy children (214 Black and 186 White) aged 6-12 years. Of these children, 68 Black and 115 White children also undertook plethysmography. Results were expressed as percent predicted according to commonly used equations for spirometry and plethysmography.

RESULTS

Black children had lower lung function for a given height compared to White children. The magnitude and direction of these differences varied according to specific outcome. In the studied age range (6-12 years) the ethnic-specific Wang equations were adequate for spirometry (mean results approximating 100% predicted in both ethnic groups). By contrast, significant differences were found between observed and % predicted plethysmographic lung volumes according to published equations derived from White children: Among the Black children, function residual capacity (FRC) and total lung capacity (TLC) were on average, 14 and 6% lower than predicted, whereas mean residual volume (RV) and RV/TLC were 4 and 10% higher. Among White children, the Rosenthal equations gave the best fit, with the exception of FRC which was, on average, 9% lower than predicted.

CONCLUSION

Spirometry equations may suffice in Black children; however, interpretation of static lung volumes in Black children is limited due to inappropriate reference equations. More appropriate plethysmographic reference equations that are applicable to all ethnic groups across the entire age range are urgently needed.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.

Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis

Most proteomic studies use liquid chromatography coupled to tandem mass spectrometry to identify and quantify the peptides generated by the proteolysis of a biological sample. However, with the current methods it remains challenging to rapidly, consistently, reproducibly, accurately, and sensitively detect and quantify large fractions of proteomes across multiple samples. Here we present a new strategy that systematically queries sample sets for the presence and quantity of essentially any protein of interest. It consists of using the information available in fragment ion spectral libraries to mine the complete fragment ion maps generated using a data-independent acquisition method. For this study, the data were acquired on a fast, high resolution quadrupole-quadrupole time-of-flight (TOF) instrument by repeatedly cycling through 32 consecutive 25-Da precursor isolation windows (swaths). This SWATH MS acquisition setup generates, in a single sample injection, time-resolved fragment ion spectra for all the analytes detectable within the 400-1200 m/z precursor range and the user-defined retention time window. We show that suitable combinations of fragment ions extracted from these data sets are sufficiently specific to confidently identify query peptides over a dynamic range of 4 orders of magnitude, even if the precursors of the queried peptides are not detectable in the survey scans. We also show that queried peptides are quantified with a consistency and accuracy comparable with that of selected reaction monitoring, the gold standard proteomic quantification method. Moreover, targeted data extraction enables ad libitum quantification refinement and dynamic extension of protein probing by iterative re-mining of the once-and-forever acquired data sets. This combination of unbiased, broad range precursor ion fragmentation and targeted data extraction alleviates most constraints of present proteomic methods and should be equally applicable to the comprehensive analysis of other classes of analytes, beyond proteomics.

Assessment of personal exposures to optical radiation in large entertainment venues

Workplace exposure to optical radiation from artificial sources is regulated in Europe under the Artificial Optical Radiation Directive 2006/25/EC implemented in the UK as The Control of Artificial Optical Radiation at Work Regulations 2010. The entertainment environment often presents an extremely complex situation for the assessment of occupational exposures. Multiple illumination sources, continuously changing illumination conditions and people moving during performances add further complexity to the assessment. This document proposes a methodology for assessing the risks arising from exposure to optical radiation and presents detailed case studies of practical assessment for two large entertainment venues.

Occupational UVR skin protection by make-up

New legislation has been introduced in the Member States of the European Union, covering worker exposure to artificial optical radiation. Use of make-up could reduce the ultraviolet hazard level and provide additional protection for skin against UV radiation (UVR). This is particularly important in entertainment and filming where intentional exposure of the actors and presenters to the very intense light sources may be required for extended periods of time. This document presents the assessment of UVR protection of make-up used in entertainment and demonstrates that the protection level varies considerably for different luminaires and application techniques. An important practical implication of this finding is that make-up alone cannot be considered as a reliable protection measure against skin exposure to actinic UV.

Utility of multivariate analysis in support of in vitro metabolite identification studies: retrospective analysis using the antidepressant drug nefazodone

The utility of multivariate analysis in in vitro metabolite identification studies was examined with nefazodone, an antidepressant drug with a well-established metabolic profile. The chromatographic conditions were purposefully chosen to reflect those utilized in high-throughput screening for microsomal stability of new chemical entities. Molecular ion, retention time information on groups of human liver microsomal samples with/without nefazodone was evaluated by principal component analysis (PCA). Resultant scores and loadings plots from the PCA revealed the segregation and the ions of interest that designated the drug and its corresponding metabolites. Subsequent acquisition of tandem mass spectrometry (MS/MS) spectra for targeted ions permitted the interrogation and interpretation of spectra to identify nefazodone and its metabolites. A comparison of nefazodone metabolites identified by PCA versus those found by traditional metabolite identification approaches resulted in very good correlation when utilizing similar analytical methods. Fifteen metabolites of nefazodone were identified in beta-nicotinamide adenine dinucleotide phosphate (NADPH)-supplemented human liver microsomal incubations, representing nearly all primary metabolites previously reported. Of the 15 metabolites, eight were derived from the N-dealkylation and N-dephenylation of the N-substituted 3-chlorophenylpiperazine motif in nefazodone, six were derived from mono- and bis-hydroxylation, and one was derived from the Baeyer Villiger oxidation of the ethyltriazolone moiety in nefazodone.

Comprehensive analytical strategy for biomarker identification based on liquid chromatography coupled to mass spectrometry and new candidate confirmation tools

A comprehensive analytical LC-MS(/MS) platform for low weight biomarkers molecule in biological fluids is described. Two complementary retention mechanisms were used in HPLC by optimizing the chromatographic conditions for a reversed-phase column and a hydrophilic interaction chromatography column. LC separation was coupled to mass spectrometry by using an electrospray ionization operating in positive polarity mode. This strategy enables us to correctly retain and separate hydrophobic as well as polar analytes. For that purpose artificial model study samples were generated with a mixture of 38 well characterized compounds likely to be present in biofluids. The set of compounds was used as a standard aqueous mixture or was spiked into urine at different concentration levels to investigate the capability of the LC-MS(/MS) platform to detect variations across biological samples. Unsupervised data analysis by principal component analysis was performed and followed by principal component variable grouping to find correlated variables. This tool allows us to distinguish three main groups whose variables belong to (a) background ions (found in all type of samples), (b) ions distinguishing urine samples from aqueous standard and blank samples, (c) ions related to the spiked compounds. Interpretation of these groups allows us to identify and eliminate isotopes, adducts, fragments, etc. and to generate a reduced list of m/z candidates. This list is then submitted to the prototype MZSearcher software tool which simultaneously searches several lists of potential metabolites extracted from metabolomics databases (e.g., KEGG, HMDB, etc) to propose biomarker candidates. Structural confirmation of these candidates was done off-line by fraction collection followed by nanoelectrospray infusion to provide high quality MS/MS data for spectral database queries.

Instrumental and experimental effects in LC-MS-based metabolomics

The experimental complexity of a metabolomics study can cause uncontrolled variance that is not related to the biological effect being studied and may distort or obscure the data analysis. While some sources can be controlled with good experimental techniques and careful sample handling, others are inherent in the analytical technique used and cannot easily be avoided. We discuss the sources and appearance of some of these artifacts and show ways in which they can be detected using visualization and statistical tools, allowing appropriate treatment prior to multivariate analysis (MVA).

Dimensionality reduction and visualization in principal component analysis

Many modern applications of analytical chemistry involve the collection of large megavariate data sets and subsequent processing with multivariate analysis techniques (MVA), two of the more common goals being data analysis (also known as data mining and exploratory data analysis) and classification. Classification attempts to determine variables that can distinguish known classes allowing unknown samples to be correctly assigned, whereas data analysis seeks to uncover and understand or confirm relationships between the samples and the variables. An important part of analysis is visualization which allows analysts to apply their expertise and knowledge and is often easier for the samples than the variables since there are frequently far more of the latter. Here we describe principal component variable grouping (PCVG), an unsupervised, intuitive method that assigns a large number of variables to a smaller number of groups that can be more readily visualized and understood. Knowledge of the source or nature of the variables in a group allows them all to be appropriately treated, for example, removed if they result from uninteresting effects or replaced by a single representative for further processing.

Instrumental and experimental effects in LC-MS-based metabolomics

The experimental complexity of a metabolomics study can cause uncontrolled variance that is not related to the biological effect being studied and may distort or obscure the data analysis. While some sources can be controlled with good experimental techniques and careful sample handling, others are inherent in the analytical technique used and cannot easily be avoided. We discuss the sources and appearance of some of these artifacts and show ways in which they can be detected using visualization and statistical tools, allowing appropriate treatment prior to multivariate analysis (MVA).

Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragment ions. Absolute quantification of identified species was linear within a concentration range of 10 nM-100 microM and was achieved by spiking into total lipid extracts a set of synthetic lipid standards with diheptadecanoyl (17:0/17:0) fatty acid moieties, representing six common classes of glycerophospholipids. The automated analysis of total lipid extracts was powered by a robotic nanoflow ion source and produced currently the most detailed description of the glycerophospholipidome.

Complexity among constituents of the HLA-B*1501 peptide motif

Analysis of peptides derived from HLA class I molecules indicates that thousands of unique peptides are bound by a single molecular type, and sequence examination of the pooled constituents yields a motif which collectively defines the peptides bound by a given class I molecule. Motifs resulting from pooled sequencing are then used to infer whether particular viral and tumor protein fragments might serve as class I-presented peptide therapeutics. Still undetermined from a pooled motif is the breadth or range of peptides in the population which are brought together to form the pooled motif, and it is therefore not yet known how representative of the population a pooled motif is. By employing hollow fiber bioreactors for large-scale production of HLA class I molecules, sufficient peptides are produced to investigate individual subsets of peptides comprising a motif. Edman sequencing and mass spectrometric analysis of peptides eluted from HLA-B*1501 reveal that many peptide sequences fail to align with either the N- or C-terminal anchors predicted for the B*1501 peptide motif through whole pool sequencing. These analyses further reveal auxiliary anchors not previously detected and peptides significantly larger and smaller than the predicted nonamer, ranging from 6 to 12 amino acids in length. These results demonstrate that constituents of the B*1501 peptide pool vary markedly in comparison with one another and therefore in comparison with previously established B*1501 motifs, and such complexity indicates that many of the peptide ligands presented to CTL cannot be predicted using class I consensus motifs as search criteria.

Microdissection, microchip arrays, and molecular analysis of tumor cells (primary and metastases)

Advances in biotechnology and bioinformatics are offering promise for new breakthroughs in gene discovery and elucidation of gene function. At present, many candidate genes related to cancer pathogenesis have been identified in several types of human cancer, yet frequently their function remains elusive. This is particularly true as it relates to the progression of human cancer. This landscape could change dramatically, however, as technological innovations and improvements continue to revolutionize these fields. High-throughput molecular approaches are emerging, which may become accurate, automated, and cost-effective. For example, DNA arrays on microchips are under development with numerous applications, including the ability to screen genes rapidly for mutations and to study patterns of gene expression on a large scale. Automated systems for microdissection and sequencing are also in their implementation stages. Commensurate with their integration and evolution, these information and technological tools have the potential to offer a more comprehensive understanding of multiple genetic and cellular alterations occurring during cancer initiation, development, and progression. Ultimately, this fundamental knowledge can provide strategies for intervention, prevention, and early diagnosis. This is a US government work. There are no restrictions on its use.

The Clementine bistatic radar experiment

During the Clementine 1 mission, a bistatic radar experiment measured the magnitude and polarization of the radar echo versus bistatic angle, beta, for selected lunar areas. Observations of the lunar south pole yield a same-sense polarization enhancement around beta = 0. Analysis shows that the observed enhancement is localized to the permanently shadowed regions of the lunar south pole. Radar observations of periodically solar-illuminated lunar surfaces, including the north pole, yielded no such enhancement. A probable explanation for these differences is the presence of low-loss volume scatterers, such as water ice, in the permanently shadowed region at the south pole.

The characterization of proteins and peptides by automated methods

A suite of software programs called the BioToolBox is described. The primary purpose of the BioToolBox is to facilitate the characterisation of proteins and peptides using data acquired by IonSpray mass spectrometry and tandem mass spectrometry. As an example, the characterization of a 50 KDa protein (transcription termination factor-rho) is described. The programs which comprise the BioToolBox produce complementary information which is exchanged between the software modules.

Error-tolerant protein database searching using peptide product-ion spectra

A method for matching proteins in databases with unknown samples using data derived from peptide product ion masses is described. The power of the method is due to the speed of analysis and to the ability to locate proteins in a database even when the experimental data show anomalies due to derivatization or post-translational modification.

Photodynamic therapy for chest wall recurrence in breast cancer

Photodynamic therapy is the use of a sensitizer (dihematoporphyrin ethers) which is preferentially retained in tumor cells and activated by subsequent light delivery resulting in a selective tumoricidal effect. Between 1986 and 1989, we treated 20 patients with photodynamic therapy for chest wall recurrence of breast cancer. Responses were seen (20% complete response, 45% partial response, 35% no response), but the duration of response was short (average 2.5 months). Complications, in decreasing frequency, included pain, ecchymoses, blistering, ulceration and necrosis in the area of tumor involvement on the chest wall. One patient required skin flap reconstruction for full thickness necrosis. A limitation to this mode of therapy is that the sensitizer currently used is activated by light at a wavelength of 630 nm. This light can penetrate to a tissue depth of only 0.5 to 1.0 cm; thus, deeper disease cannot be treated. Future research must focus on the development of a clinically useful photosensitizer that can be activated by light at longer wavelengths and thereby achieve deeper tissue penetration. This would greatly expand the patient population for which this therapy is useful.

[A new method in the analysis of vitreous fluorophotometry. Results in early diabetic retinopathy]

New methodology to analyze posterior vitreous fluorophotometry (PVF) data is described. Values for D, fluorescein vitreous diffusion coefficient and P, permeability of the blood retinal barrier (BRB) to fluorescein are obtained. D was found to be significantly greater in diabetic patients with minimal retinopathy compared with either controls or patients with no retinopathy. P values were not significantly different between diabetic patients and controls or between diabetic subgroups, confirming the absence of breakdown of the BRB, as assessed by PVF, in early diabetic retinopathy.

Bronchoscopic phototherapy at comparable dose rates: early results

Photodynamic therapy is a recently introduced treatment for surface malignancies. Since January 1987, 10 patients with endobronchial neoplasms have had bronchoscopic photodynamic therapy at similar dose rates (400 mW/cm) for total atelectasis (2), carinal narrowing with respiratory insufficiency (2), or partial obstruction without collapse (4). Two patients underwent photodynamic therapy as a preliminary to immunotherapy. Histologies included endobronchial metastases (colon, ovary, melanoma, and sarcoma, 1 each; and renal cell, 3) and primary lung cancer (3). The 2 patients with total atelectasis had complete reexpansion after photodynamic therapy, which permitted eventual sleeve lobectomy in 1. Carinal narrowing was ameliorated in the 2 patients seen with inspiratory stridor, thereby permitting hospital discharge. Endoscopically resected fragments after photodynamic therapy exhibited avascular necrosis. These data support further controlled studies of photodynamic therapy by thoracic surgical oncologists to define its limitations as well as to improve and expand its efficacy as a palliative or surgical adjuvant.

Photon migration in layered media

Surface emission profiles and related functions are computed for particles (photons) migrating within a semiinfinite medium containing a surface layer whose absorbance differs from that of the underlying layer. Photons are assumed to be inserted at a single point on the surface. In certain cases distinct features appear in the emission profiles which enable determination of the thickness of the top layer and of the absorption coefficients of both layers. Computations are performed to provide estimates of parameter ranges for which the presence of one layer distorts photon emission profiles from the other. Several ancillary functions are calculated, including the absorbance profile as a function of depth, the expected path length of photons that are reemitted at a distance rho from the point of insertion, and the average depth probed by those reemitted photons.

Localization of magnetic interictal discharges in temporal lobe epilepsy

Three young adults with intractable complex partial seizures were studied by electroencephalography, magnetoencephalography, and electrocorticography. Interictal electroencephalographic (EEG) spikes for each patient were grouped according to their morphological characteristics and distribution across channels. Mapping of simultaneously recorded magnetoencephalographic signals produced dipolar patterns from which the three-dimensional locations of equivalent current dipoles were calculated, whereas the mapping of EEG spikes showed single regions of electronegativity. The magnetic spikes were localized to the anterotemporal lobe, and the EEG spikes were localized somewhat anterior or posterior to the magnetic spikes. The magnetoencephalographic findings corresponded well with intraoperative electrocorticographic and depth-electrode findings of discharging areas located over the lateral temporal lobe and on the basal and mesial surfaces of the temporal cortex.

A simple, computer-assisted system for measuring latencies of contact placing

A system for measuring the latencies of two components of contact placing, limb withdrawal and landing, is described. Timing functions are performed by a microcomputer, which also records and displays the latencies, and summarizes the data. Procedures for testing contact placing are also described, and data collected from morphine-treated, Long-Evans hooded rats are presented.

Model for laser Doppler measurements of blood flow in tissue

A theory is developed which relates quasi-elastic light scattering measurements to blood flow in tissue micro-vasculature. We assume that the tissue matrix surrounding the blood cells is a strong diffuser of light and that moving erythrocytes, therefore, are illuminated by a spatially distributed source. Because the surrounding tissue is considered to be stationary, Doppler shifts in the frequency of the scattered light arise only from photon interactions with the moving blood cells. The theory implies that the time decay of the photon autocorrelation function scales proportionally with cell size and inversely with mean translational speed. Analysis of multiple interactions of photons with moving cells indicates the manner in which spectral measurements additionally are sensitive to changes in blood volume. Predictions are verified by measurements of particle flow in model tissues.