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

Freestone, Jack / Noble, William S / Keich, Uri

2024

Abstract: 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). ...

Abstract	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.
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00399
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Article ; Online: Reinvestigating the Correctness of Decoy-Based False Discovery Rate Control in Proteomics Tandem Mass Spectrometry.

Freestone, Jack / Noble, William Stafford / Keich, Uri

Journal of proteome research

2024

Abstract: 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 ...

Abstract	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
Language	English
Publishing date	2024-04-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00902
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Article ; Online: Bridging the False Discovery Gap.

Ebadi, Arya / Freestone, Jack / Noble, William S / Keich, Uri

Journal of proteome research

2023 Volume 22, Issue 7, Page(s) 2172–2178

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Algorithms ; Databases, Protein ; Proteomics/methods ; Tandem Mass Spectrometry
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.3c00176
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Article ; Online: Group-walk: a rigorous approach to group-wise false discovery rate analysis by target-decoy competition.

Freestone, Jack / Short, Temana / Noble, William Stafford / Keich, Uri

Bioinformatics (Oxford, England)

2022 Volume 38, Issue Supplement_2, Page(s) ii82–ii88

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Peptides/chemistry ; Proteomics/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Peptides
Language	English
Publishing date	2022-09-20
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac471
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Article ; Online: The sector is ready, and the community needs Australian alcohol and other drug treatment services to ask about sexuality and gender identity.

Freestone, Jack / Mooney-Somers, Julie / Hudson, Suzie

Drug and alcohol review

2021 Volume 41, Issue 1, Page(s) 39–42

Abstract: 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, ... ...

Abstract	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.
MeSH term(s)	Australia/epidemiology ; Female ; Gender Identity ; Humans ; Male ; Sexual Behavior ; Sexual and Gender Minorities ; Sexuality ; Transgender Persons
Language	English
Publishing date	2021-08-09
Publishing country	Australia
Document type	Journal Article
ZDB-ID	1080442-0
ISSN	1465-3362 ; 0959-5236
ISSN (online)	1465-3362
ISSN	0959-5236
DOI	10.1111/dar.13367
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Article ; Online: Individual level peer interventions for gay and bisexual men who have sex with men between 2000 and 2020: A scoping review.

Freestone, Jack / Siefried, Krista Joy / Prestage, Garrett / Hammoud, Mohamed / Molyneux, Angus / Bourne, Adam

PloS one

2022 Volume 17, Issue 7, Page(s) e0270649

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Bisexuality/psychology ; HIV Infections ; Homosexuality, Male/psychology ; Humans ; Male ; Sexual Behavior ; Sexual and Gender Minorities
Language	English
Publishing date	2022-07-15
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0270649
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Article ; Online: Playing at the edges, navigating sexual boundaries, and narrating sexual distress; Practices and perspectives of sexuality and gender diverse people who use GHB.

Freestone, Jack / Bourne, Adam / Layard, Eloise / Prestage, Garrett / Murray, Joel / Siefried, Krista J

The International journal on drug policy

2022 Volume 108, Page(s) 103811

Abstract: 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 ...

Abstract	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.
MeSH term(s)	Female ; Gender Identity ; Homosexuality, Male ; Humans ; Male ; Sexual Behavior ; Sexual and Gender Minorities ; Sexuality ; Sodium Oxybate ; Substance-Related Disorders/epidemiology
Chemical Substances	Sodium Oxybate (7G33012534)
Language	English
Publishing date	2022-08-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2010000-0
ISSN	1873-4758 ; 0955-3959
ISSN (online)	1873-4758
ISSN	0955-3959
DOI	10.1016/j.drugpo.2022.103811
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Article ; Online: Understandings, attitudes, practices and responses to GHB overdose among GHB consumers.

Freestone, Jack / Ezard, Nadine / Bourne, Adam / Brett, Jonathan / Roberts, Darren M / Hammoud, Mohamed / Nedanoski, Anthony / Prestage, Garrett / Siefried, Krista J

Harm reduction journal

2023 Volume 20, Issue 1, Page(s) 121

Abstract: 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 ... ...

Abstract	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.
MeSH term(s)	Humans ; Sodium Oxybate ; Australia ; Drug Overdose/prevention & control ; Mental Disorders ; Attitude
Chemical Substances	Sodium Oxybate (7G33012534)
Language	English
Publishing date	2023-09-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2146691-9
ISSN	1477-7517 ; 1477-7517
ISSN (online)	1477-7517
ISSN	1477-7517
DOI	10.1186/s12954-023-00857-z
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Article ; Online: Controlling for pleasure and risk: The experiences of sexuality and gender diverse people who use GHB.

Freestone, Jack / Prestage, Garrett / Bourne, Adam / Ezard, Nadine / Race, Kane / Nedanoski, Anthony / Murray, Joel / Siefried, Krista J

The International journal on drug policy

2022 Volume 105, Page(s) 103747

Abstract: 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. ...

Abstract	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.
MeSH term(s)	Drug Overdose/epidemiology ; Drug Overdose/prevention & control ; Gender Identity ; Humans ; Pleasure ; Sexual Behavior ; Sexuality ; Sodium Oxybate
Chemical Substances	Sodium Oxybate (7G33012534)
Language	English
Publishing date	2022-05-25
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2010000-0
ISSN	1873-4758 ; 0955-3959
ISSN (online)	1873-4758
ISSN	0955-3959
DOI	10.1016/j.drugpo.2022.103747
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Article ; Online: Participatory design of an improvement intervention for the primary care management of possible sepsis using the Functional Resonance Analysis Method.

McNab, Duncan / Freestone, John / Black, Chris / Carson-Stevens, Andrew / Bowie, Paul

BMC medicine

2018 Volume 16, Issue 1, Page(s) 174

Abstract: Background: Ensuring effective identification and management of sepsis is a healthcare priority in many countries. Recommendations for sepsis management in primary care have been produced, but in complex healthcare systems, an in-depth understanding of ... ...

Abstract	Background: Ensuring effective identification and management of sepsis is a healthcare priority in many countries. Recommendations for sepsis management in primary care have been produced, but in complex healthcare systems, an in-depth understanding of current system interactions and functioning is often essential before improvement interventions can be successfully designed and implemented. A structured participatory design approach to model a primary care system was employed to hypothesise gaps between work as intended and work delivered to inform improvement and implementation priorities for sepsis management. Methods: In a Scottish regional health authority, multiple stakeholders were interviewed and the records of patients admitted from primary care to hospital with possible sepsis analysed. This identified the key work functions required to manage these patients successfully, the influence of system conditions (such as resource availability) and the resulting variability of function output. This information was used to model the system using the Functional Resonance Analysis Method (FRAM). The multiple stakeholder interviews also explored perspectives on system improvement needs which were subsequently themed. The FRAM model directed an expert group to reconcile improvement suggestions with current work systems and design an intervention to improve clinical management of sepsis. Results: Fourteen key system functions were identified, and a FRAM model was created. Variability was found in the output of all functions. The overall system purpose and improvement priorities were agreed. Improvement interventions were reconciled with the FRAM model of current work to understand how best to implement change, and a multi-component improvement intervention was designed. Conclusions: Traditional improvement approaches often focus on individual performance or a specific care process, rather than seeking to understand and improve overall performance in a complex system. The construction of the FRAM model facilitated an understanding of the complexity of interactions within the current system, how system conditions influence everyday sepsis management and how proposed interventions would work within the context of the current system. This directed the design of a multi-component improvement intervention that organisations could locally adapt and implement with the aim of improving overall system functioning and performance to improve sepsis management.
MeSH term(s)	Delivery of Health Care/standards ; Humans ; Primary Health Care ; Sepsis/pathology ; Sepsis/therapy
Language	English
Publishing date	2018-10-11
Publishing country	England
Document type	Journal Article
ISSN	1741-7015
ISSN (online)	1741-7015
DOI	10.1186/s12916-018-1164-x
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