Analysis of Tandem Mass Spectrometry Data with CONGA: Combining Open and Narrow Searches with Group-Wise Analysis.

Searching for tandem mass spectrometry proteomics data against a database is a well-established method for assigning peptide sequences to observed spectra but typically cannot identify peptides harboring unexpected post-translational modifications (PTMs). Open modification searching aims to address this problem by allowing a spectrum to match a peptide even if the spectrum's precursor mass differs from the peptide mass. However, expanding the search space in this way can lead to a loss of statistical power to detect peptides. We therefore developed a method, called CONGA (combining open and narrow searches with group-wise analysis), that takes into account results from both types of searches─a traditional "narrow window" search and an open modification search─while carrying out rigorous false discovery rate control. The result is an algorithm that provides the best of both worlds: the ability to detect unexpected PTMs without a concomitant loss of power to detect unmodified peptides.

Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry.

Traditional database search methods for the analysis of bottom-up proteomics tandem mass spectrometry (MS/MS) data are limited in their ability to detect peptides with post-translational modifications (PTMs). Recently, "open modification" database search strategies, in which the requirement that the mass of the database peptide closely matches the observed precursor mass is relaxed, have become popular as ways to find a wider variety of types of PTMs. Indeed, in one study, Kong et al. reported that the open modification search tool MSFragger can achieve higher statistical power to detect peptides than a traditional "narrow window" database search. We investigated this claim empirically and, in the process, uncovered a potential general problem with false discovery rate (FDR) control in the machine learning postprocessors Percolator and PeptideProphet. This problem might have contributed to Kong et al.'s report that their empirical results suggest that false discovery (FDR) control in the narrow window setting might generally be compromised. Indeed, reanalyzing the same data while using a more standard form of target-decoy competition-based FDR control, we found that, after accounting for chimeric spectra as well as for the inherent difference in the number of candidates in open and narrow searches, the data does not provide sufficient evidence that FDR control in proteomics MS/MS database search is inherently problematic.

Understandings, attitudes, practices and responses to GHB overdose among GHB consumers.

BACKGROUND: Gamma-hydroxybutyrate (GHB) is used at disproportionately high rates within sexuality and gender diverse communities and carries a high risk of overdose. GHB overdose can result in death. Internationally, recent increases in GHB overdoses have been observed. Coronial reviews of GHB-related death highlight the pivotal roles that bystanders to GHB overdose play in preventing fatality. No research has examined, in detail, how bystanders respond to GHB overdose. This qualitative study was conducted among people who use GHB and explored how they responded upon witnessing a GHB overdose experienced by someone else. METHODS: Interviews were conducted with 31 sexuality and gender diverse Australian residents reporting three or more occasions of GHB use in the previous 12 months. Participants were asked questions about witnessed GHB overdose, their actions and decision-making processes throughout overdose. Data were analysed thematically. RESULTS: Participants described witnessing GHB overdose, commonly in private settings involving sexualized GHB use. Variable definitions of GHB overdose were reported, ranging from GHB-induced symptoms of distress to comatose intoxication. Drastic actions to keep someone alert and responsive post-GHB ingestion were reported; these included the administration of stimulant substances and citrus. Decisions to call or not call for emergency medical services (EMS) were influenced by many circumstantial variables. In most instances, an EMS call was resisted and response practices deviated from established first aid protocols. CONCLUSIONS: GHB overdose prevention and response training programs targeting people who use GHB are urgently required. These education interventions ought to address inaccuracies that inform street remedies for GHB overdose, teach people how to safely check breathing and response, promote basic first aid principles and address barriers to contacting EMS.

Bridging the False Discovery Gap.

Controlling the false discovery rate (FDR) among discoveries from a tandem mass spectrometry proteomics experiment using target decoy competition (TDC) controls only the proportion of false discoveries in an average sense. Thus, for any particular analysis, even with a valid FDR control procedure, the proportion of false discoveries (the FDP) may be higher than the specified FDR threshold. We demonstrate this phenomenon using real data and describe two recently developed methods that help bridge the gap between controlling the expected or average rate of false discoveries and the empirical rate (FDP). The FDP Stepdown method controls the FDP at any desired confidence level, and the TDC Uniform Band provides a confidence, or upper prediction bound, on the FDP in TDC's list of discoveries.

Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition.

MOTIVATION: Target-decoy competition (TDC) is a commonly used method for false discovery rate (FDR) control in the analysis of tandem mass spectrometry data. This type of competition-based FDR control has recently gained significant popularity in other fields after Barber and Candès laid its theoretical foundation in a more general setting that included the feature selection problem. In both cases, the competition is based on a head-to-head comparison between an (observed) target score and a corresponding decoy (knockoff) score. However, the effectiveness of TDC depends on whether the data are homogeneous, which is often not the case: in many settings, the data consist of groups with different score profiles or different proportions of true nulls. In such cases, applying TDC while ignoring the group structure often yields imbalanced lists of discoveries, where some groups might include relatively many false discoveries and other groups include relatively very few. On the other hand, as we show, the alternative approach of applying TDC separately to each group does not rigorously control the FDR. RESULTS: We developed Group-walk, a procedure that controls the FDR in the target-decoy/knockoff setting while taking into account a given group structure. Group-walk is derived from the recently developed AdaPT-a general framework for controlling the FDR with side-information. We show using simulated and real datasets that when the data naturally divide into groups with different characteristics Group-walk can deliver consistent power gains that in some cases are substantial. These groupings include the precursor charge state (4% more discovered peptides at 1% FDR threshold), the peptide length (3.6% increase) and the mass difference due to modifications (26% increase). AVAILABILITY AND IMPLEMENTATION: Group-walk is available at https://cran.r-project.org/web/packages/groupwalk/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Playing at the edges, navigating sexual boundaries, and narrating sexual distress; Practices and perspectives of sexuality and gender diverse people who use GHB.

BACKGROUND: Research addressing sexualised use of GHB to date has largely focussed on gay and bisexual men's GHB use in the context of chemsex, this research has highlighted risks and experiences associated with sexual violence. No studies have included people of diverse sexualities and genders and documented reported practices to ensure mutually gratifying and consensual sex in the context of sexualised drug use (SDU). METHODS: Semi-structured interviews were conducted with 31 people from sexuality and gender diverse communities living in Australia who reported three or more occasions of GHB use in the previous 12 months. Participants were asked about their use of GHB for sex, their experiences of GHB sex and their approaches to negotiating sexual boundaries. Data were analysed thematically. RESULTS: Most participants valued the sexual possibilities enabled by disinhibitory components of GHB and were cognisant of respecting other's sexual boundaries in the context of GHB sex. Participants reported strategies to ensure communication prior to and throughout GHB sex. However, several participants narrated experiences of GHB sex that they felt were distressing and, in some circumstances, sexually violent. In most instances participant's resisted terminology of sexual violence or non-consent as descriptors of their experience and none reported accessing sexual violence services. CONCLUSION: Positive strategies to facilitate sexual communication prior to and throughout GHB sex should be reflected in health promotion and service level responses to promote affirmative and continuous consent among people who use GHB for sex. Education initiatives to help people engaged in SDU to recognise and respond to sexual violence if it occurs ought to be prioritised.

Individual level peer interventions for gay and bisexual men who have sex with men between 2000 and 2020: A scoping review.

BACKGROUND: Peer-led interventions are central to the global HIV response for gay and bisexual men who have sex with men [GBMSM]. Since the year 2000, technological advancements in HIV and an increased response to the health disparities faced by GBMSM outside of HIV, have contributed to the expanding scope of their content and delivery. This review sets out to characterise the evidence base for individual level peer interventions for GBMSM, overview approaches to implementing and evaluating them and identify future priorities for their delivery and evaluation. METHODS: A scoping review methodology was applied and evaluations of peer programs for GBMSM published in peer reviewed journals were identified via subject heading and keyword searches across five electronic databases. Titles and abstracts were reviewed, and full texts were assessed against eligibility criteria. A coding framework was used to extract data from included studies against intervention implementation and evaluation components. RESULTS: A total of 38 studies evaluating peer led interventions against effectiveness outcomes were deemed eligible for inclusion and coded into four intervention modalities; peer counselling [n = 6], groupwork programs [n = 15], peer navigation [n = 7] and peer education [n = 10]. Most addressed HIV [n = 32] and across intervention modalities, evaluations demonstrated compelling evidence of significant effect. Intervention effects on broader indicators of psychosocial wellbeing were not extensively evaluated. Expertise regarding the implementation and evaluation of peer interventions addressing HIV among GBMSM ought to be leveraged to expand the scope of peer intervention to meet the diverse health and wellbeing needs of GBMSM.

Controlling for pleasure and risk: The experiences of sexuality and gender diverse people who use GHB.

BACKGROUND: GHB is used among some sexuality and gender diverse populations at elevated rates, however little qualitative research has explored GHB use among these populations with regards to diverse contexts, settings, practices, and experiences of use. Internationally, harms relating to GHB overdose appear to be increasing. Research outlining consumers' experiences of GHB-related pleasures and their strategies to reduce harms may inform GHB education and intervention responses. METHODS: N = 31 participants reporting three or more occasions of GHB use within the previous 12 months were recruited via digital advertising and snowball methods. Semi-structured interviews were conducted, data were transcribed and analysed in NVivo using a thematic framework analysis. Emergent themes were charted, and divergences and convergences were considered with regards to the sexuality and gender identities of participants. RESULTS: Pleasures associated with GHB were described in relation to the sensation of the GHB high and experiences of intimacy, and connection. GHB was used to enhance socialising and sex in domestic, private, and commercial venues. Participants prioritised terminology of 'control' when describing their practices associated with GHB dosing, measuring, timing and peer moderation. Most participants reported personal experience of GHB overdose with loss of consciousness. CONCLUSION: Participants' near-ubiquitous experience of GHB overdose highlights ongoing education needs around overdose prevention. Efforts must target people new to GHB use who appeared particularly susceptible to overdose. Inconsistencies in understandings around GHB overdose, the perceived severity of overdose and the differences between GHB and its precursors GBL and 1,4-BD, highlight potential focus areas of future education responses. Further research is required to better understand consumers' experiences of sexual violence in the context of GHB use.

The sector is ready, and the community needs Australian alcohol and other drug treatment services to ask about sexuality and gender identity.

Sexuality and gender diverse Australians are a priority population in federal and state-based alcohol and other drug (AOD) strategies. Research evidence shows higher prevalence of AOD use by lesbian, gay, bisexual, transgender and queer (LGBTQ) people, riskier use and a higher proportion have accessed AOD treatment. Despite these disparities, Australian AOD treatment services do not routinely collect data on sexuality or gender identity. As a result, the treatment needs, experiences and outcomes of LGBTQ people remain largely invisible. The Australian Bureau of Statistics' recently released standardised indicators for the recording of sex, gender, variations of sex characteristics and sexual orientation presents an opportunity for the AOD sector to implement inclusive data collection as a foundational step towards achieving policy priorities for LGBTQ people. This commentary includes an implementation case study from the New South Wales non-government AOD treatment sector, where sexuality and gender identity indicators have been collected since 2016.