I would like to begin by acknowledging and celebrating the first Australians on whose traditional lands we meet, the Ngunnawal and Ambrie people, and pay my respects to elders past and present. It is great to see everyone here tonight. It's really, I think, also nice to be able to welcome our expert panel and moderator who will be coming out in just a second on stage. We have been spending the last year celebrating our first 75 years. We have seen students return to on-campus learning and held some special celebration. It's nice to have been able to do that this year. And we have had alumni events around the world totaling at least 75, hopefully to be achieved in the not too distant future. We have reflected on our history and really reflected on what we have achieved over the last 75 years and the people who have helped us make those achievements. ANU was founded in 1946 in a very interesting time, a time which is, I guess, even a more extreme version of what we are facing in 2022. But in a spirit of post-war optimism to help Australia realize its potential as the world recovered from World War II, ANU was set up. 75 years later, we are here. Very timely discussion this evening as we recover from, of course, a different global crisis and reflect on the role of universities. Our expert panel and moderator this evening will be exploring tonight's theme, The University of the Future. With an emphasis on looking to the future, tonight's panel's discussion will look at the next 75 years and address some important questions. How will our university and others look in another seven and a half decades? How are we ensuring our graduates are ready for the future of work, noting that probably about half, assuming trends stay on the same path of our students today will be here in 75 years at the twilight of their lives. And most importantly, how is the higher education sector meeting the needs of our rapidly changing world, which in 75 years, if you kind of project the current trends, is going to be quite a bit different in ways that may not be entirely great for, I think, a humanity that lives peacefully on the planet. In the short term, we know that the next decade is going to be turbulent, or maybe I know, because I can see the winds of change in higher education. Higher education, of course, has been around for just under a thousand years in a university form. And I think over the next 10 years we're going to see shape, a revolution that brings together an intense global competition in higher education around teaching and learning that goes well beyond universities, but also into industry and other organizations.  And the absolute way that universities were connected on research and teaching 200 years ago has been somewhat unwound over the last 30 or 40 years. And I'm not quite sure where that's going to go. And I'm curious to listen to our panel today to think about it. 75 years from now, I may even be more confident about the future, because I think universities exist in a form for a reason. But again, I look forward to hearing from our panel. Our leading panel this evening from across the higher education sector, both locally and abroad, is going to be able to think about visions for the future of the university. Tonight's debate will be carefully preserved amongst a suite of curated items to be sealed in a time capsule this Friday at our closing ceremony, the final event to mark our 75th anniversary. The time capsule will be sealed and reopened in 2046 and our 100th year, and it will be interesting to see how we fare our panel fares about predicting the future. Universities have and have had a truly significant place in society, easily forgotten. I do believe that they are critical in the economic, the global, the social renewal post COVID, but to the future of human prosperity. I would now like to introduce our moderator for this evening, Professor Giselle Behrens, Provost of Massey University in New Zealand. Giselle is an internationally recognized historian, former Fulbright scholar who has published widely on the aspects of settler colonial and indigenous histories. She has worked for the Waiatangi Tribunal and has served as president of the New Zealand Historical Association. She has led large and complex senior academic executive roles in Australia and in New Zealand. Giselle is committed to advancing the agenda around equity and access to higher education and is a strong advocate for the critical role played by modern universities in creating social, cultural and intellectual capital for public benefit and economic well-being. I couldn't think of a better academic to be joining us tonight, traveling across the ditch to moderate tonight's discussion. I'm also very pleased that Giselle is able to hang around the university for a few days and I have found discussing with her, and I have been able to do this for the last couple years, the future in the near term of higher education very fascinating. So she will be just perfect for this. So please, without further ado, join me in welcoming Professor Giselle Behrens. Giselle? Kia ora koutou katoa. Nga mihinui kia koutou. Nga mihinui kete rangatira. Tiena koe. Warm greetings from Aotearoa, New Zealand, and thank you very much Vice-Chancellor. I wish to acknowledge this evening the Nangawal and Numbri people, the traditional owners of the land on which we meet this evening, and to pay my respects to their elders past, present and emerging. Thank you for the opportunity to speak on your country, and thank you also to the ANU for the invitation to participate in the 75th anniversary celebrations of this wonderful university. My role this evening is to briefly set the scene and to moderate this evening's debate. The format of the event is that each of our speakers will have the opportunity to offer some thoughts, and then we'll engage in a general discussion. We've also set aside some time for questions and answers from the audience in the final part of our session this evening, and thank you to those who have already offered questions in advance. We have those. Tonight we are defining the University of the Future as a general proposition to refer to the idea and the mission of the University at large, rather than any specific institution. And I'd like to say right at the outset that the future is notoriously difficult to predict. Indeed, as many of you will be aware, predicting the future is even more challenging when we consider that any accurate forecast hinges on variables that are almost wholly unpredictable, and in some cases unimaginable, and that the process of prediction itself might influence the future in ways that could be wrong-headed or ill-conceived. So in other words, we risk being deterministic rather than being open-minded and free from bias. That being said, however, one of the best ways to imagine the future is to look to the past. When the ANU was established 75 years ago, the world was a very different place, and the founding of this university was part of a clear agenda to build national intellectual capability and capacity. Conceived to serve Australia's post-war needs, the ANU was purposefully established to deliver quality education, advanced research, and postgraduate training at world-class levels. Indeed, over the long arc of the 20th century, universities have played critical roles in national efforts of reconstruction, especially after periods of crisis, and through their research, they have also advised governments and communities on how to build back better. While the context in which universities operate has changed since the 1940s. Think of the massification of higher education, the increasing demand for degree credentialing, especially in the global south, the increasing diversity among students, increased expectations on universities by employers, by governments, and by students. In other respects, many aspects of the university and indeed the academy, as it was then, are still recognisable now. It is often said that in the future, universities will face multiple challenges, the continuing expectation of producing fit-for-purpose graduates for the changing world of work, advancing and protecting the research-teaching nexus, the demand for even more customized modes and paces of learning, the importance of equity and access, the rise of for-profit providers, and the imperative to leverage big data, learning analytics and new technologies to innovate and improve the centrality of the student experience. It is frequently said too that the COVID-19 pandemic has exposed the fragility of the traditional university operating model, especially with massive disruption to international education and the global pivot to online hybrid and blended modes of learning and teaching. In addition, I think the rise of right-wing populist politics around the world, the ubiquity of information via social media and internet-based platforms, and the normalization of free market economic policy, prioritizing individualism over common good outcomes, present real challenges to universities. And all of this comes at a time when climate change and environmental degradation, along with the likelihood of managing future pandemics, are widely acknowledged as the real and pressing crises of our time. However, I want to suggest that these challenges define and describe our current moment and our present existential crisis, not the future term ahead of us and certainly not the longer term. So this evening, we want to move beyond this narrative to imagine the university in around 2097. Thinking for the longer term demands that we ask more fundamental and less context-sensitive questions such as what will be the purpose and role of the university in 75 or even 100 years' time, what will it look like, and who will it serve, how will our universities continue to matter in terms of our civic and our democratic life, or will, as Ronald Barnett has contended, the university of the future continue to evolve and exist as a dynamic project in a state of becoming rather than ever being one static idea or form. Ronald Daniels, the president of Johns Hopkins University, has recently argued that universities have four essential functions. First, they provide access in ways that encourage social mobility. Second, they educate democratic citizens. Third, they create expert knowledge. And finally, they encourage students and citizens to engage in dialogue across difference. So while these four purposes are not particularly new or novel, I would argue that the constellation of these purposes is very important, especially at a time when elite institutions risk often recreating existing inequalities, while other universities are being pressured to replace more liberal education agendas with a stronger vocational focus. Our purpose tonight, then, is to imagine the university of the future, the university on the cusp of the next century. And tonight we have a superb panel of four experts who will each speak to the proposition of imagining the university of the future, and I'm going to invite each of them on stage as I briefly introduce them to you. First of all, I'd like to introduce to you distinguished professor Genevieve Bell, who's a renowned anthropologist, technologist, and futurist. Genevieve is best known for her work at the intersection of cultural practice and technology. Development and Genevieve is the director of the School of Cybernetics and holds the Florence Violet McKenzie Chair here at the ANU. Professor Sherman Young is Deputy Vice-Chancellor Education and Vice-President of RMIT University, a scholar of media communication and cultural studies. Sherman's research focuses on the impact of new technologies on media policy cultures and industries and how new technologies have been applied in the higher education sector. Professor Michelle Ryan is the inaugural director of the Global Institute of Women's Leadership here at the ANU. Her research examines the social and psychological drivers of workplace, gender and equalities. And Michelle's research has uncovered significantly the idea of the glass cliff whereby women and members of other minoritised groups are more likely to be placed in leadership positions that are risky or indeed are precarious. I'd also like to introduce to you this evening Dr Timo Henkel, who's a Senior Lecturer of Economics and a Research Fellow in the Centre for Applied Macroeconomic Analysis here at the ANU. Timo studies the determinants of bounded rationality and the effects of such behaviour on inflation and macroeconomic policy amongst other things. I'd like to welcome our guests onto the stage this evening. Great, now we're sitting down. Great. Okay, so given the intro and the scene setting for this evening, I'm going to pose to our panellists a question that relates back to the university of the future. And Gerardine, because you are right on my left, I'm going to go to you first. So, Gerardine. Giselle. Given that universities have... No, Giselle, one more time. Genevieve. Genevieve. Genevieve. Genevieve. Genevieve. Genevieve. Genevieve. Giselle. Genevieve. I've got it. I've got it this time. Genevieve. Genevieve. Given that universities have defined themselves as places of knowledge, creation and discovery, how might the university of the future define itself? I think that's such a delightful question, Giselle, in the context of that unfolding of the scenery, and I think in the context where Brian Stardust is out this evening. So for me in thinking about what is the purpose of the university of the future, that question does at least one really important piece of work, which assumes there is one. I think it's sometimes easy to imagine the university will be gone in 100 years' time, and I think that's the wrong answer. For me in thinking about what the role and purpose of it is, I kind of want to take three threads in. One of them is, I often think when I'm asked about the future, about my very favorite futurist whose line is, the future's already here, it's just unevenly distributed, and I think the provocation in that is always if you look around you and you know what you're looking for, you can see seeds of the future. So I wonder in that context what the pandemic in particular has taught us about the things that universities do well and are special. I suspect one of the things that was hardest for universities during the pandemic was actually we've been embodied communities for a really long time, and what the pandemic compelled us to have to be was disembodied, and I think that's been hard. So there's the question for me about what has the present taught us about what the future would look like, and then I think there's a little bit about the political economy of universities which both you and Brian dwelled on as you know what brought universities into existence, what kept them in existence, and in whose interest was that done. And for me I think it then turns on what are the stories we want to tell about who we are. One of the ways universities get I think unfairly described as ivory towers, this notion of being kind of exceptional, singular, somehow better than everything sitting over here, the custodians of goodness and righteousness. And I wonder if there's a different set of metaphors we might talk about to describe who we are that help answer the question. And for me the metaphor I keep coming back to, and it was one that was provoked for me by a colleague of mine in New South Wales by the name of Angie Abdullah, who is an Aboriginal design strategist and talks about country-centric design. And she often talks about the estuary as a place of meaningful activity, a place that is neither land nor ocean, neither sort of quite stable through which things constantly flow and through which you know salt and freshwater meet and where many things happen in those intersections. And I wonder if we imagine universities as places through which things flowed and places that made possible certain kinds of flows where there's also a deep memory, because I do think universities have a particular relationship to time, time and embodiment. And I wonder if in answering the question about who will we be and who will our key stakeholders be and what would our future look like? For me it's about what's the story we want to tell about ourselves about what our role is and I don't think it's a long way of saying this. I'm not sure we get to cling to the notion that we are distinctive anymore, I think we have to be able to unpack the why of that and then I suspect our future is actually not about how we think of ourselves as exceptional but how we think of ourselves as part of a set of relationships and who we want to invite onto our campuses, into our buildings, into our classrooms and how we want to assume that people will flow through those and back out again. So for me it's about those pieces you know what have we learned in the last three years about what makes us us, what does the nature of the political economy tell us about who we need to be and then what's the story we want to tell about what would make us interesting. It's a beautiful response and particularly with that metaphor of the estuary, an estuary with you know deep time associated with that so fabulous. Thanks Genevieve, you've you've you know put out there I think a number of fantastic concepts that I know the rest of the panel and I'm sure the audience will pick up on as well. We're allowed to riff on Genevieve. You are indeed, go for it or violently disagree with me. I don't disagree with you at all. I guess it was a great starting point because I wonder and let me use probably inappropriate words. I wonder if grammatists out there please forgive me. I wonder if the university is a verb rather than a noun though because it's constantly in a state of evolving and becoming and the the analogy and I'll be full of analogies tonight for which I apologize in advance the analogy that springs to mind is is the phone and the the original telephone was fixed in to a place it had a wire coming out of the wall something in the first incarnation there was an operator which connected you and it's it was very very different from this device which we all have in our pocket here but we still call it a phone so I wonder if there's an element of that in universities in that there are things that we call universities now and Don Dawkins might have a lot to answer for that that perhaps we would not have considered universities in 1200 or 1300 etc etc in which case to me the question is well what is what is the essence of the university that remains and I think you've you've identified some of the things that are part of it and I'm going to throw into the mix if if the essence of a phone is communication I wonder if the essence of a university is transformation I'm going to leave it there well that's a it's a great provocation Sherman thank you for that so can I just kind of push you a little further on that just to throw you a specific question thinking about the university of the future what if the learning journeys through the university were to be entirely flexible and customizable and thinking about also what that would mean for the university academic or what we currently think of as the university scholar yeah that's that's an interesting question and I actually had a moment to reflect on that one thank you Giselle but to me there's probably different appetites for that type of learning journey so I don't want to dismiss the cohort based learning which has a whole lot of value for a whole lot of learners and students you know there's there's a lot of value you know in stereotypically for undergraduate students in learning in a group and and going through together and building networks etc etc and the type of flexible learning journey to describe won't appeal to everybody and nor should it but I think it is one that more and more learners may or may not wish to to engage with so I think yes universities need to pursue it and we need to find ways to make those types of learning journeys available to those learners who might want to engage in self-paced self-directed learning in all sorts of individualised ways what does that do for an academic role I don't think by itself it does anything for an academic role that we shouldn't be thinking about any way uh and the uh the I told you we're gonna do use analogies tonight the analogy I'm going to use use here is that we we think of academics um to use a cricket analogy as all rounders we think of them as having a balance of research teaching and engagement skills and we expect to have a team for the most part entirely comprised of all rounders whereas a good cricket team as we all know will have batters and bowlers and a couple of all rounders and it's the team itself that actually needs to be able to succeed rather than every single member of it being able to school a century take five wickets etc etc so I think we need to start thinking about specialisations in roles within the academic space more broadly and then within the teaching specific part of that I'm very conscious that the models that are often in deeply embedded in university teaching are centuries old and perhaps don't have the relevance that they might have right now so um we all we all don't love lectures um I'm probably not speaking for everybody but but many of us don't love lectures as a as a pedagogical approach um I know one of your your former colleagues Marnie Hughes Warrington did some work here and did the the attendance heat maps etc here at ANU and we we know that students don't love lectures either yet for some reason um we still call our academics lecturers which seems a bit bizarre to me whereas maybe we should be conceiving of the teaching roles as you know curator facilitator mentor learning designer assessor and and reconceiving of the roles to be more diverse and more enabling of the types of pedagogies and types of learning that make sense in the 21st century so the the long answer to your question Giselle is specifically I don't think those learning journeys are the only things that should drive a reconsideration of the academic role I think we need to be reconceiving of those academic roles anyway right okay thank thanks human um I'm just going to pause there for a wee bit because as you were speaking I was watching the facial expressions of colleagues and I'm thinking um you know just to push back of a little bit on that what does that do to the research teaching nexus of the university in terms of the you know what some might think of is the defining value proposition of of the university when you start to decompose the academic workforce in that kind of way and I'm not wishing to sound orthodox here I'm just asking the question about it's a really it's a really good question and I think we have to reconceive of that what that research teaching nexus might look like and you might go back to Boyer's scholarships and think you know discovery application integration teaching and and and certainly there's ways to to engage in those scholarships of application integration which you could argue are research focused that are more leaning towards the teaching space so there's there's certainly that approach that is is one quick answer the the other thing to think about which is the other the other answer that my education colleagues often give me is that there is a deep scholarship of learning and teaching so there is a research teaching nexus within the discipline of teaching itself which can provide value and and that added dimension to the academic role so but it is a really good question I think there's there's right it's an area that's ripe for actual good good constructive conversation around what an effective research teaching nexus should look like but yeah absolutely can I push of course so I'm struck in thinking about the cricket analogy I'm a tragic for those of you who don't know me well this is gonna be an awful conversation for you and I um one of the things I'm always really struck by as someone who spent the bulk of my career in industry is that there tends to be uh regimes of value inside universities that mean that researchers are treated very differently than than teaching intensive faculty um I think this is a bit like the oh it wasn't until 2021 that we had a fast bowler captain our cricket team because only batsmen could do that so we had a regime of value inside cricket in world Australian cricket indeed well you know we're in your Australian university but there's a little bit here about how do you imagine because I think one of the the features of a university of the 22nd century would need to be one where we are attentive to how we think about either continuing to stitch those together or unstitching them in an either context how we do a better job of balancing people's notions about what is kind of the real work there because looking underneath all of that there are implicit value statements there there are and and there's there's two kind of responses I'll have the first is around you know when I articulated those those some of the perhaps multi-faceted teaching roles which I didn't expand on there are kind of research focused elements of it so if you're a curator or an expert in that teaching space then there is definitely a research focus on the second part of it is that many universities at least a couple that I've worked at have worked very hard to diminish that hierarchy so promotions policies etc reward and recognition frameworks it's entirely possible at the last two universities to get promoted on teaching alone and that's the way it should be you know we should have a properly egalitarian democratic approach to how we how we deal with reward and recognition but it is a really important conversation so if you were going to say that in a way that made that true you would say at the last two universities about it's even been possible to be promoted if all you did was research and that's that's always that's always been the case but you need to turn that it's the it's even possible so that it starts to be agreed so that's a little bit about even the language we choose about those values reinforce them over time yeah absolutely correct correct and on on that note I'm gonna move us along just in terms of thinking about you know that longer term vision and sherman you just mentioned a couple of you know key terms there around equity and so on Michelle thinking about the universe of the future how can that university and its abstract sense as we're discussing this evening ensure fairness and equity given that universities carry huge amount of historical baggage and I've got a follow-up to that you know how radical could universities be in the future in terms of really realising equitable outcomes and especially for those who've been historically marginalised or excluded from the academy I wish I had a simple answer for you Giselle I mean I think if we knew that we would have sort of done it already but but I think the idea that you know if we're looking at a university of the future it should be one that is fair that is equitable that is safe and I think part of the question is well how do we get there what do we have to change does it have to be radical and my expertise is in the area of gender but I'm not just talking about gender it could be on the basis of you know cultural and linguistic diversity on indigeneity class I think is quite a big one sexuality all of the ability all of those sorts of things and the intersections of those and I think it's really important to think what we mean by equitable and what we mean by fair and I think historically we've often talked about equality in terms of access just who is here on the ground what are the numbers look like and if we go back 75 years you know if we compare 1947 to now it's a radically different university you know there are you know we've had 50 percent women for at least 30 years for example you know there is much more access in in terms of social mobility for people from working classes and things like that so there has been a lot of change in terms of just access but that's not a linear change either in some ways if I think of when I first came to university this this university actually in the early 90s a good I mean Barrett feels 30 years ago feels like quite a long time now I'm not sure so much has changed in in that 30 years certainly not visibly but I think when we talk about equality we shouldn't just be talking numbers we shouldn't just be counting the number of women that are on our campus or counting the number of female professors although we still need to do that because it is you know horrendously low and should be higher but we should be thinking about more complex notions of what equality and fairness and diversity looks like so what are the experiences of you know historically underrepresented groups what are their experiences on campus what are their experiences once they leave as well so for example again we know that women do just as well their grades are just as good but we also know as soon as they hit the workplace they take a cut of 20% of their salary compared to men so are we not only how are we treating them on campus but how are we setting them up for the future but I think also what we have to do is say you know if universities are creating or teaching the leaders of tomorrow the employees of tomorrow you know shaping the institutions of tomorrow as well are we doing that in a way that makes sure that they are fair and equitable and safe as well so I think we have to do a lot of work there and some of it comes to what you know both Sherman and Genevieve were talking about is what do we value what is research excellence what is knowledge what are our classic texts you know how do we think about those things because all of those things all of those decisions about what we teach what we reward what we value all of those things have the either I guess the possibility to reinforce the status quo and the inequalities that exist now or they have a chance to challenge them and to change them and those sorts of things so when we talk about equality it's not just a numbers game it really is thinking about what we value and what we do so it is things about you know decolonializing the curriculum we hear a lot about that and but really thinking about what that means and really saying what do we value what do we want our you know students of the future our employers of the future our leaders of the future to value and reward as well so there's no answer there sorry so I know because I mean you you you're right I think what you are touching on of course is that universities are you know both reflective of the wider society of which they are apart but we also have the audacious promise I think of challenging and possibly starting with ourselves right and so you you referenced decolonizing the curriculum which in many parts of the world is is a way to start to do that and I think in some respects possibly all of the kinds of inequity that you cited we're probably just getting our heads around what it means to really reshape and rethink our existing structures yeah I think absolutely the other thing that I would also say is when we think about the future of universities there's a big variety in universities and what higher education institutions look like and when we talk about social mobility and change and and achieving equality I think you know different universities approach that in different ways and different universities reinforce that in different ways as well often inadvertently but I do think that regional universities vocational universities teaching focus universities actually often do a lion's share of the work when it comes to social mobility and change and I think that's important to note and I think there is something you know and not talking about specific universities but just the structure of of higher education and how we look at it we have to make sure that elite does not equal elitism you know so so our elite universities our strong universities aren't you know bastions of elitism and we have to make sure and see how we pull those two things apart and you make a really good point there Michelle around the importance of universities a university being part of an ecosystem so that there is that diversity there is that breadth and ultimately there is there's choice for students I think because universities have different missions so I think I think that's a really prescient point thank you thank you Timo I'm going to I'm going to go to you've been very patient thank you very unusual for me we've been touching on research and teaching throughout the conversation this evening and while it's widely recognized that both research and teaching have public and private good qualities and benefits these shift over time is economic and social context shift and change as well so thinking about the university of the future what do you think the role of government in the higher education sector should be so you're asking an economist to make a prediction 75 years out indeed we can't even predict inflation a quarter out or GDP so um tall order I'm a big proponent as I've said elsewhere in different fora of the Humboldtian ideal model of education which is one that marries research and teaching right it's where I guess teaching is guided by research and and research should ultimately be unbiased and independent of of various influences religious economic ideological political and and so what we're really going for is is an unconditional academic freedom right whilst we're investigating the world and trying to understand it these these are what I would argue are humanistic ideals that are underpinning all this and it should be right free thinking knowledge should be formed on the basis of logic and reason and empiricism and you know avoid any kind of subjugation to authority and tradition and dogma I mean those those are lofty ideals that I think will him from the Humboldt set out in the early 2019th century when he founded the University of Berlin or now the Humboldt University and and they are largely reflective of the kind of society that we're trying to create or live in or ideals that we're trying to foster and and and encourage and nurture in society at least I would argue that most most members of society feel that way what I think Humboldt had in mind was uh the the idea from enlightenment that that there are two important concepts and one is the individual and the rights of the individual and the other is is creating a world citizen which acknowledges that we are a member of society and so really it's about a balance right between what's good for the individual um and how that individual fits into a greater collective and of course that then ties in with the general question of what the role of government is and it's all about I think a healthy balance which again is an outcome of enlightenment I'd say is that government has a role to play but it it can't it can't be too strong and really what I think the primary role of government is now and always should be is to preserve those ideals within the higher education sector as it does within society uh at large how that is done and achieved and implemented is I think a larger question um not just for us in some ways but for for many more scholars um going forward in the next 75 years and beyond um to which I have no no real answers to be honest um but the government will invariably in some way or another be involved in the higher education sector and it should be as I said on the one hand there's I guess a regulatory aspect to it to ensure academic freedom uh the the pursuit of free thoughts free speech and so on um and at the same time also financial again it's about a balance this is where I I like that estuary uh metaphor I think some free enterprise within the higher education sector is useful but we can't rely alone or excessively on on private money because that's going to compromise I think some of the ideals that that home bolts set out initially um so finding that balance I think is going to be really difficult and it may change over time as your your question seemed to suggest um for example I'll just and then I'll stop there for example if the artificial intelligence the AI revolution really takes place and we basically end up in a kind of sort of neo-athenian world where much of the menial jobs are actually done by robots or not uh so robots as opposed to human slaves then we we quickly run into a situation where we have to ask well who owns those robots who owns those factors of production that raises a question well should we tax them should the benefits from that factor of production uh just as for example land arguably should be uh should that be socialized and then that's something that's uh would arguably benefit universities um and the whole idea of of learning and knowledge creation and knowledge transmission uh in society so I can't predict what this what the world is going to look like in 75 years but I'm confident that the government will have a role to play and it's going to be a significant role and that leads us back to that question of accountability doesn't it I mean to whom is the university uh of the future or will the university of the future be accountable yeah can I ask a question and this would be an anthropologist talking to an economist which is always dangerous uh in my discipline we're always really interested in the space that exists between the articulation of cultural ideals and the reality of cultural practices so you manifested the humbled ideal and I'm sitting there going huh so what went wrong because I don't think that's a whole lot of people's experiences of the universities over the last 200 years so if that's the cultural ideal of universities can you talk a little bit about what you think the cultural practice of universities is and why there's a such a delta there I'm asserting that there is a delta to the start of there as an anthropologist I'm pretty clear there's cultural ideals and cultural practice you've said a cultural ideal and there's a cultural practice over here in the future is that gap as big yes well the gap is sometimes bigger sometimes smaller it's also I think not always equal across various universities or in various countries for example I think a fundamental problem with the universities is and I think that's what some of my co-panelists here have pointed out is that there is an inherent elitism around um around higher education and and universities and the kind of people who populate universities and and universities have been abused by elites and those who are in power and I think that has in turn for example compromised some of those ideals that you think are not actually lived in real experience so so it's not just about universities alone and what universities can change on their own in order to preserve those ideals it's it's a greater conversation about how society works and and only then can universities slot into uh into into that debate we cannot I think uphold those ideals on our own if if it's not met on fertile ground within society at large can I can I jump in there with a comment because I think the Humboldt and your ideal is a fairly recent one in some ways and if you go back a little bit further then universities were about elites um and they were about ideology uh and they were about the you know the the training of public servants etc etc and I mean the chinese university history was all about elitism and etc etc so the french university system is very much still that way so there is a cultural baggage that we carry as an as institutions of learning that that are pulling us and pushing us in different directions and you know it's a really interesting conversation have right now to to your point Genevieve around that delta has probably been shifting ebbing and flowing throughout time and we are luckily enough able to engage in that conversation around how we want that ebb and flow to happen which is great and and that baggage that you refer to Sherman is both part of the value proposition that we have uh and also Michelle to your point uh some of the stuff that weighs us down as well so there's a there's a kind of a contradiction there isn't there in terms of the the current identity of who the university is I wonder just going back Genevieve to your metaphor of the history which I love thinking about how that ebb and flow might help us think about what the university of the future could look like in regards to the you know the kind of the porosity of that if I can mix my metaphors here yeah so I mean one of the things that attracts me to that language in particular is that I mean Estre's not to belabor that image that when they do have a a cyclicality to them that's knowable you know they they surge and contract there are different kinds of categories of things that exist and but it's also about the flow through and I think for me I'm always really struck in thinking about the ways in which universities and I think it's a plural universities in the future not the university of the future I think it's a plural university for many of this same set of reasons I think part of what will make universities of the future not just successful but thrive is the ways in which they are porous to different kinds of lived experiences but also to different kind of notions of what excellence looks like you know I'm I'm often struck having spent such a lot of my career outside of the university that for a place that in some ways entertains notions of that ideology and Humboldt is an ideology it's also a surprisingly restrictive place in terms of its ability to see other kinds of value other kinds of scholarship other forms of production and thinking about how we would recognize the works of intellectual and knowledge production that are happening inside industry that are happening inside government that happen inside non-university organizations and how we would see those as things that could flow through and inform universities and how we would think about the people that are here going to other places and doing work elsewhere for me there's a little bit about how we not only anticipate that but actively encourage it I think it's a little bit about how do you and sort of know that those things are part and parcel of what it means to be here so that it is in fact about the range of lived experiences in the place and the sort of the in some ways the more robust that is now granted one of the consequences of having an increasingly diverse collection of people is that you have increasingly large interesting conflict I think we don't talk about that terribly often but in my lived experience diversity and inclusion brings a degree of people not speaking the same language in multiple ways and so part of what you then have to do is think about how you're going to manage that in a productive way but I think for me the encouragement of imagining that it is multiple kinds of scholarship knowledge production ways of engaging in learning the kinds of people that will be here for how long and what they imagine they are getting while they are here and what they are leaving with feels like it ought to be more expansive not to put too fine a point on it I think that idea of conflict is interesting that diversity brings conflict I would say that conflicts always there but by giving some people access to a stage on which to talk or bringing them on a level playing field actually just allows them to and to be clear I think conflicts are good ideas exactly so productive discomfort that is yeah so I think the conflict has always been there but there's actually been a raising up of a voice that actually allows a conversation to happen about the conflict instead of just having it there and not be spoken about so I think that's interesting I keep while I'm sitting here I'm reflecting on Sherman's idea about what the essence of his phone is and what the essence of universities are and I think that is a kind of really interesting thing about whether it is transformation or Genevieve what you were sort of alluding to or is it knowledge and what is that knowledge or you know is it all of those sorts of things as well and yeah just trying to think about how do we bring that down to it it's a sort of thing and if it is about this sort of journey through and if it is about us you know what are we transforming are we transforming students that are coming through are we you know transforming information into practice so we you know and just I think there's something there that I it's interesting and and you know I'm just conscious you know two weeks ago I went to University of Australia conference and the new minister did his first public kind of like talk and he talked about he didn't use the word transformation but he talked about his own transformation through education and he talked about the transformative impact of researchers in response to the COVID pandemic and and so it was very much about you know the sector being agents of transformation and and and I I certainly hear that from the stories from students their lives have been transformed but I think importantly for me it's not just the individual transformation it's the role of universities in transforming society which I think is equally important and it's it's something that I think needs to be deeply embedded in what we do because if we don't do that then why we're here you know we can do it through individual students and individual research but we have to develop whether it's developing students so they can become leaders to transform society or whether we pursue progress as an institution to really embed inclusion diversity sustainability etc etc I think it's a moral responsibility for the universities not sure where that came from just just brief response to Genevieve earlier you said that there are very narrow metrics of excellence for example in the higher education sector of universities and and I I totally agree and I think these narrow metrics have been imposed for I'm not even sure the right reasons but they they absolutely compromise what I think are some of those Humboldtian ideals namely freedom of research and freedom of thought what what the current practice really is doing it's is leading to an utter homogenization of of departments of a way of thinking of an academic approach it is reducing diversity dramatically at least I can see this in in my discipline and neighboring disciplines and and that is highly problematic and that's because for example there are budgetary pressures that that force competition in an inefficient way if you've heard it here from an economist that competition is not always great that that competitive forces that prevent exactly the pursuit of these these ideals that I was referring to earlier so I there is there are certain things that I think we would like to see different in universities but again we cannot do those in isolation without without proper government policy without the right support from from society from from the people who elect those governments and and so on and I think it comes back to a question that you raised that I'm not quite sure that we answered around accountability so who are we accountable for so to you know is it government is it students as customers is it you know a wider society is it you know those sorts of things and I think trying to work out you know yet that accountability and what that accountability will look like in the future I feel like we've sort of we're a little bit in the present at the moment but thinking about where that accountability is and I think there are a lot of different models about what that looks like if I so look at the US for example where that accountability is you know where that student debt is and all of those sorts of things I think there's some cautionary tales there about you know the balance between government and and private offerings and all of those sorts of things but yeah I think I think that sort of certainly raises that issue of that accountability is that you know do we go lofty and say it's to knowledge or you know to those sorts of things but yeah a balance of all of those and and just trying to thread together some of these threads which is really interesting you know if we take the estuary and the permeality of the various stakeholders and then questions around efficiency the operating models that we have don't lend themselves to a future of efficiency and effectiveness we're still stuck in a semester model that may not be the most effective and efficient our approach to pedagogy is still interesting we need to perhaps think about how we can partner with industry in ways to to really embed the learning in ways that are more effective and efficient you know and we need to be open to those sorts of things and instruct me we're talking about when I was thinking about the estuary model and and what we might do the one because sorry it's on my mind at the moment the recognition of prior learning for example is something that is incredibly inefficient across the whole sector and for some reason we have this elite view that someone who may have worked for 20 years as a chief marketing officer doesn't deserve recognition for one course of study in a MBA and that speaks to those notions of elitism but we need to be more permeable in order to get the learning from across all of those experiences and and understand that there are different types of learning which helps with the models of efficiency that we might need to think of. The flexibility importantly also extends I think to the whole notion of disciplines right I mean we we are so siloed in the way we conduct research and teach and and learn which again I think is probably counter to the Humboldtian ideals but importantly I think prevents our students from from tackling some other really big issues which require increasingly I'd say a system approach complexity thinking which is interdisciplinary transdisciplinary and requires tools that I think are are not really taught at universities at the moment and that's perhaps one area where universities can take a bigger step in trying to to achieve that and I know there are working groups at the moment for example at the ANU one of them about sort of graduate attributes referring precisely to interdisciplinary learning and teaching I would like to see a lot more of that and it also acknowledges going back to the the debate about the role of the government it acknowledges that in a system approach we cannot easily measure what the marginal benefit or product of any one activity is everything depends on everything sounds very hard and it is but it does make that much more difficult to try to isolate what the value of any one activity is so we need to embrace that more an anthropologist and economist met in a bar is that the beginnings of a joke or no seriously though it's not a funny joke it could be a funny joke I totally depends on how many gin and tonics I totally agree with you Timo and and you know I've been trying to smash together the disciplines for for quite some time in in the institutions I've worked with and the the question I keep asking and I don't get an answer to despite the fact that in in my role I should be able to get an answer to it why is it so hard and so why is it so hard well I think this is where the academics actually do have to take a close look at themselves in the mirror there is a lot of vanity there is a lot of well so there's a little bit the other answer to this would be to say as much as we should be decolonizing our curriculums we may need to expand our imaginations about what it means to be an academic what it means to be in a university in partly from Michelle's impulses around how we make it a more equitable and accessible place but I also think because one of the ways we have used disciplinary activity is as a form of boundary maintenance so you know one of the things that we we know is that you know culture and disciplines are defended in the breach right it is much easier to say you're not like us because you don't do these things and the disciplines then become a way of protecting flows of money so I think resources from government grants think ways of ensuring promotions and advancement think ways of saying this thing we recognize this thing we don't I mean you know again I came from the outside and one of my most extraordinary moments in coming back to Australia was having one of our largest funding bodies explain to me that I needed to explain to them the 18-year great gap in my correct my CV and the first question was did you have children like I had a career in industry they're like so you had a career gap I mean I became a vice president in an American tech company like yes but you had a career gap like no I think I had a career somewhere else they're like yes but you've had a gap and so it became this really extraordinary moment of having to realize that for a large part of the constituent organization that defined academic excellence in this country there was no capacity to imagine one might have enacted Humboldtian scholarship in somewhere other than a university and so for me there's a little bit that says here if we really want to imagine what the universities of the future look like we're also going to need to contend with not quite a sure I want to call them competitors in the economic sense but with the other organizations who have stakes in the things that we think we do best so what does it mean to imagine a world in which industrial research labs actually are enacting scholarship in ways we would understand they're investing in it deeply they're doing it over multiple years they care about rigor they publish their results they work in interdisciplinary teams so they frequently don't call them that they just call them project teams and they have an enormous amount of money and wherewithal and resources to spend there so how do we think about those how do we think about the fact that in some countries around the world it's government departments that are driving the innovations in everything from meteorological activity to economic theory to ideas about artificial intelligence frankly because some of the places its government spending that money so there's a little bit here that says the competitive landscape for the universities of the future the places that are doing the things that we thought only we could do well and not just other universities they're organizations whose internal logics and regimes of value and ways of being are profoundly different than ours and if we don't think about them as occupying our space and of wanting to it's why it's the fresh water salt water fish thing for me it's like at least acknowledging that they're there and how we think about that as a productive thing rather than imagining that what goes on in industry isn't real research or what goes on in some other kind of place can't be real because it's not what was the language oh intellectually free it has freedom of speech and freedom of thought so imagining that only universities do that and that that's the quality of what makes kind of a future state thing for me feels like it's a potentially dangerous mental model not that disagree with the humble ideals it's just that I don't want them to become a thing that blinds us to the realities of what also was happening in our ecosystem or there's also lots of other structures surrounding universities that just reinforce those sorts of things as well so I'm thinking academic the academic publishing industry for example so you talked about funding set up in a particular way I mean to the extent that our currency as academics is publications you know in within this industry and that's set up in a very particular way so both in what in terms of what it values how it's all set up in terms of discipline by discipline and and you know just that process by which that happens and the fact that you have to call anything that isn't that a non-traditional research output took me a while to work out what that one was to an NTRO I don't know what that is is that good the answer is it isn't or at least not in many ways and so there's a little bit there about again it's how do we even think about unpacking the language we use to talk to ourselves about who we are is also a set of conversations we need to have with our future selves if we want to find a pathway to that absolutely and and not just thinking about the language but how we describe ourselves to others most importantly and you know and the observations that you've made about the disciplinary identity that we cling on to sometimes feels it very much at odds with the student journey through the university because it can sit in complete tension or dissonance with that kind of pathway counter yeah sorry it's I mean it's it doesn't there's not just a dissonance with the students journeys but also with lived reality so often I have students come to me and they've seen someone occupy a certain job or doing a job and they want to know how they got there and it's almost always with lots of roundabouts and very circuitous it's it's not like it used to be where you studied one discipline and you it was pretty clear what you were end up doing it is much more free flowing now and and I think students feel lost because they just don't know they have a rough idea vague idea of the kind of work that they want to do or the kind of space that they want to occupy but they don't really know how that translates into the path in university to get there and I suspect it's the same degree of confusion may sit with some of our government colleagues and with industry who are like I need a person that does this thing I've no idea what you call them like I don't know where on the website I would find them all locate them so it's a little bit about how we make ourselves visible yeah I think so yeah piece of that yeah I'm going to take us now to some questions and we do have some questions that we received in advance so just picking up on that latest discussion point we have a question which was submitted by by one of our students here do you think that universities should push back against growing pressures to gear education towards employment we've touched on this a little bit already and more specifically how should the Australian university sector change to better support international students so there's two two questions there and there's a particular focus on international students in that second one I think the first part of that question um do you think universities should push back against growing I'm happy I'm happy to start with that one if you want my short answer is no I think uh to a certain extent a large number of our students come to universities because they have an employment outcome in mind now I'm from RMIT which is you know probably got a slightly different focus from ANU but certainly when I speak to our students and we've done a lot of research for our students there is an an absolute goal around employment I would also say that government expects that from us and we are funded because there's an expectation that we are skilling our learners and our graduates to be able to have employment having said that I think to Timo's point the reality is the direct pathway to employment is a short term fraught one and as universities we have the responsibility to educate and you know cliche um our students not just for the first job but for their life of working and and those skills those transferable skills are not ones that you necessarily teach in a you know bachelor's of machine learning or something but are probably broader humanities based skills I'm betraying my my disciplinary sorry my my kind of discipline background as well but they're probably broader human skills that will ground you and provide a broader foundation for employment um the the other reflection is that that broader education which I think is the subtext of the question that we aspire to I would argue actually makes for better employment outcomes anyway so it's going to happen irrespective of whether we focus directly on it or whether we um actually try and avoid it yeah so it takes us back to the point that you made earlier Timo around graduate attributes and amplifying and highlighting those in in terms of skill acquisition I completely agree I mean employability is important um I've just come back from spending almost two decades in the UK um and just some reflection they're very good at measuring outcomes and funding universities on the basis of those outcomes so if there's a metric that can be measured it will be measured in the UK um and employability is an important metric but it's also very interesting for me to observe how then that can be played um and then how that can be interpreted as well so uh one of the metrics was graduate salary for example um which was interesting and we found that Oxford and Cambridge for example would have a much higher graduate salary than a regional sort of teaching university and then they'd say okay more money to Oxford and Cambridge now one of those things is that you know there's the backgrounds that the people from Oxford and Cambridge are so totally different from those other universities and so even if those students had never gone to Oxford and Cambridge they may very well have started off in their dad's business on a good salary anyway so it wasn't necessarily the university that was adding that value on whereas someone that came from a real working class value background even though they might have earned 10 000 less than their Cambridge counterparts it's still 20 000 more than their parents ever did and so so that's not to say that um employment isn't important and employability is an important but I think we have to be very careful how we start to measure those sorts of outcomes and that we don't put a value on certain types of employability outcomes there's also a lot of sort of talk about well you know science graduates versus arts graduates and those sorts of things and how much we value those sorts of jobs so and welcome back to Australia Michelle you'll be pleased to know we do the same things here yeah gosh hell etc etc yeah so so so that's just I guess a bit of a cautionary tale about what we value but then how we measure that value a point well made yeah there was a second part of that question there was a second part of the question which was around uh how should the university Australian university sector change to better support international students anecdote warning ahead um I did a I did a an event with international students recently and I had was surrounded by half a dozen international students I said to them so if there's one thing I can do to improve your experience here what would it be and almost as one they said get us a job um and it wasn't necessarily when I unpacked it wasn't necessarily the employment after the degree it was the we need help during the degree as well so I think you know and that's a little bit instrumental um but it's it's certainly one thing that international students are very conscious of it's very expensive to come to Australia and leave and work and study and and I personally think there's a huge benefit for the globe in what we do with international students there's a there's a huge diplomatic relationship um building process that higher education institutions actually uh active participants in that is really important um and so I think we could do better and we we started to you know do way more in our careers areas for international students I think that's one pretty simple thing that I mean it's not simple but it's one straightforward thing that I think we could do I think it's another area in which it's not just numbers but it's also experience as well so I've got a PhD student who's still back in the UK that's doing some some work on international students and one of the things she always finds is it was like all the effort went in to get you in the door and to pay the fees and once you're there you don't feel that you're been made to belong that you're valued on all of those sorts of things so making sure again that we're not just talking about numbers and fees but we're actually talking about proper value integration and and adapting our system so not just expecting international students to adapt to the way that it is here but also for us to adapt to what it looks like to have an international cohort of students absolutely and with the you know the hiatus that we've had in the last couple of years in both Australia and New Zealand and further afield we've got the opportunity to reset that haven't we you know and and Bill Becker better it's been a really fun discussion thank you Giselle and our wonderful panel I think reflecting on the discussion tonight I can think back to 1946 when the ANU was established ANU was established as a research university only a few percent of Australians went to university at that time a very elite and elitist crowd and one would I guess reflect that that elitism still persists but in different ways the essence of the university has been sort of teased out by the panel was I think for ANU put in the motto which is first comma to know the nature of things not a race not to scoop someone but first understand and if I go back and I think about that core value and I know we've talked a bit about that that core value of understanding that goes right back to 1080 to the beginnings of a university and so I feel quite confident having listened to our panel tonight that 75 years from now that will still be a core value of ANU but I also think as we have talked about Sherman and Genevieve especially the many types of a university it's not at all clear to me that we will have 40 50 60 percent of the population taught in the future in a research intensive university because the economist in me which is thanks to my wife I think of Timo tells me that whenever there is an opportunity there are rents and teaching students has been sort of the way to fund universities other activities since World War two it doesn't really exist before that it's a post World War two thing although I guess you would find out that the lectures like Galileo used to charge his students so that he could go and invent things so it does go back further but I could easily see that changing quite dramatically and how students are involved in the university I can imagine will still be teaching people in research and interacting with probably a very rich set of stakeholders who are also doing research at the very at the more applied end but no one I think is going to do the basic foundational knowledge because there's no money in it and so it's a classic market failure it's a place where universities funded by the government as Timo said I feel pretty safe there but we may well be quite a bit smaller niche in the environment there may be a whole new of things called universities that actually don't look like what we are today so it is going to be a really interesting ride I think over the rest of my life I'm not planning to make 75 years from now but I'd like to thank our extraordinary panel and moderator for teasing out the impossible the future thank you very much


Welcome to MOOC course on Introduction to Proteogenomics. In the last lecture Mr. David Campbell, he started discussing about SWATH Atlas in various comparisons of DIA versus DDA methods. He also introduced to the concepts of DIA and the softwares and tools available for analyzing DIA data sets. The SWATH Atlas contains high quality ion libraries for use in SWATH or DIA experiments. In today's lecture you will provided an overview of the features available on SWATH MS and how you can utilize this valuable resource for analyzing your mass spectrometry data. So, let us welcome again Mr. David Campbell for his today's lecture. So, this is DIA-LQC, basically what we have is we have an ion library, we have a variety of different formats. We have a SWATH file. And the SWATH file basically says, okay, I am going to look from this mass to this mass and I am going to, you know, basically the width of each bin. And you can also compare it to a proteome. So, basically you have taken a proteome and you digest it and you have all the triptych peptides. You basically run this thing and you get this ion library, excuse me, ion library summary in tabular format. And so, these are the different criteria. Library complexity is sort of how big the library is, how many peptides, how many peptide ions. There is precursor information. So, what is the average length of the peptides in the library? How many modifications are there? What kind of modifications? Fragment characteristics, you know, what ions do you have, B or Y? How many fragments do you have per peptide? Retention time is a very important part of any sort of targeted or scheduled type analysis. You don't want to look over the entire retention time range. So how much does it vary? Is it consistent? Do you have marker peptides or these things called IRT peptides? Library completeness, you compare it to a proteome. How many of the proteins in that proteome do I cover? And library correctness. So, it turns out that there are certain things with relation to the SWATH file or relation to the actual embossies that are being reported. Is this library in fact correct? So, basically I'm going to go through these very briefly and so I have two different libraries depicted here. So, this is the PHL, the Pan-Human Library and this is again taken from all these different experiments. Everything was run on a pretty modern instrument, the A, B, Psi, X, T, T, 5600 and you can see that there are some 211,000 peptide ions, so again a peptide ion is a primary sequence plus modification plus charge and there are almost 3 million fragments. So, the other thing I have is I basically took this PHL and I applied our SWATHs. So now, because they used, they had a, when they did DDA, they were looking at wider M to Z ranges. In addition, we were looking at these 100 SWATHs and so we don't want any fragment ions in our precursor windows and what's more, we actually took the top 6 fragments. So we want to specifically take just the top 6 and so you can see that going from here to here, we didn't lose that many ions. So by applying maybe some more stringent mass filters, we didn't lose that many ions, but if you look at the number of fragments, we have way fewer fragments, almost something like 35 or 38% only of the fragments and that's because now we only have up to 6 fragments per peptide and actually, I've got ahead of myself here. So, yes, so I've, confusingly, I've put it down in this section. So this is the number of stripped peptides, we would say. So this is just the number of total peptides and again, these two numbers are pretty close, but if you look at this number 149 up to 211, those are things that we saw, say both oxidized and unoxidized or multiple charged states of the same peptide. That's actually pretty common, especially plus 2 and plus 3. So, yeah, so again, the peptide characteristics are how many peptides did we see, what sort of modifications, what percentage of the peptides are modified, things like that. This is a big one, so basically this is the number of fragments and as I told you, so this is the PHL, the average number of fragments is about 13, whereas the new library, it's exactly 6 and that's because we wanted to know, we were comparing these different softwares and we wanted to ensure that all the different software used the same peaks to do their analysis and so most of them use 6 fragments by default and so we limited our library to 6 so that they would all be on equal footing. But you can see the percentage in charge 2 and charge 3 and, you know, sometimes going from the all to the modified library, you do actually see a swing in the percentage and, you know, I don't really know why that would be, but, you know, you might expect you'd see fewer charge 3 because, you know, basically M to Z might fall below now the lowest M to Z value that we're looking for because something divided by 3 is obviously smaller than something divided by 2, but this is, it's a useful sanity check to compare to what you're expecting, are the mass ranges in my library what I would expect. So here's a difference so you can see that in their analysis they had Q3s, fragment ions up to 2,000 whereas we only took fragment ions up to 1,500 because that's what we're looking for in our SWAT. There's really not that much above it so we don't bother with it. We just look up to 1,500 because, again, we want to do our cycle time so that we can sample across the peak. So, yeah, there's all these different things and they probably, I mean, I'm showing you two guys in the back can't even see what it is, but if you're trying to assess the validity of your library it's actually very helpful and we have had a number of occurrences where this has helped us a lot. So, again, retention time is very important for analysis. So we're using something called IRT peptides and IRT peptides are peptides that you're meant to put in pretty much all of your runs and they help you to register the retention times between the runs and it just so happens for some reason that they go from negative to positive and so the reason that these show up as negative value from negative 60 to 180 is basically because they've been converted into what we call IRT space. So that's a little unusual, but it's a dead giveaway. If you're looking at a library that, you know, if these ranges don't make sense then it's a red flag to look at something. So one other thing, there's a measure of consistency. So as I mentioned, sometimes you see multiple charge states of the same ion and it turns out when you make a spectral library, the software treats everything independently and so you end up getting potentially different charges for your plus two and plus three of the same peptide. Now that doesn't make any sense from the perspective that when your peptide's eluting, it's not like your plus three elutes here and your plus two elutes here.  So you would hope that your plus two and your plus threes would be very close to each other. But it turns out that they're not. And in some cases we found libraries where these numbers are very different. So here are two libraries that are in the SWATLIS and basically, oops, sorry. And so what we're looking at is plus two and plus three charges. And so this one has a very good correlation. So having used the IRT peptides, everything is pretty much right along the diagonal. So this is basically, we take in all the peptide ions that you have the plus two and the plus three for exactly the same modified peptide and plotted them against each other. So you'd expect in a perfect world, they'd just lie down on this axis. But you see that there are some outliers and the width of this is kind of big. So you could look at this and say, well, that's actually plus or minus five minutes or plus or minus three minutes, something like that. So that can help you to decide how wide of a sort of window that you look at when you're trying to look for these things. So this is a yeast library and actually it's got a pretty strong correlation as well. Everything lies a little bit better along the axis, but we have sort of more pronounced outliers. So this is just an example of how IRT can vary. And it illustrates why we might look at this in our libraries. So this is sort of another thing. So basically, in addition to storing the retention time, these libraries have what they consider to be the best spectrum. So we've taken between, well, one and a hundred different spectra and made the best consensus that we could. So, Spectras will pick one peptide that either has the highest signal or has the lowest signal for noise depending on how you have it set up. And so all this shows is that if you pick pairs of peptides in the blue, where basically the retention time, the difference between the minimum retention time seen for this ion and the maximum retention time seen for the ion is pretty close, then you get a much better correlation between the median retention time and this best replicate spectrum. So library completeness is basically taking a proteome. So most of you, if you're working with some sort of organism, you have a proteome or a genome that you want to compare to. And this just looks at those things and says, okay, of the things that I might expect to see, of the peptides I might expect to see, of the proteins I might expect to see, how many of them do I actually see in this library? And it gives you an idea of how complete the library is. And for most of these things that the two different libraries, even though we've cut this one down, don't really vary that much. One thing that's kind of interesting to note is the average number of peptides per protein is seven, but the median peptides per protein is like 17. So it turns out that the PHL is pretty over represented in some, some proteins are over represented. You have up to say 100 peptides for that protein, including some things that are semi triptych or have miscleavages. So normally for SRM, you wouldn't want to use that type of peptide. You'd want sort of the best representative of peptides for each protein. So that's one thing we might want to do with the, the PHL is, is narrow it down a little bit. And I'll get some more evidence of that later. So actually one caveat. So basically, this is the number of triptych peptides. This is the number of perfectly triptych peptides, that match the perfectly triptych peptides here. So 20% of the entire proteome, covered in this library. We know that there is about 12,000 out of 20,000. So we know that we've only covered 60% of the proteins. So those proteins, we're just not getting perfect coverage. So, so yeah, you might think that this number is pretty small compared to the 500,000. Yeah, you may well be right. It may be a function of sort of quality criteria that were applied here. But I mean, it's a very rare mass spec experiment or set of experiments that can see 100,000 different peptides from human. So these things are actually things that are wrong with the library. And you might not think that it's possible, but it turns out that you can, you can actually have improper M disease. And because we're accepting things at SWAT Atlas, we want to make sure that people submit a database and we're then providing it for the community. We want to make sure that there's not something wrong. And so by and large, these numbers are all okay. These are things comparing the SWAT files that you provided with the actual library. And so generally speaking, you look at all these things and there's like four or five of them that stand out to you. And as somebody who actually works with these libraries quite a bit, I have used this a number of times. Anyway, so I know that's pretty boring. Here's a little bit of a description of why we might want to have good libraries. So as a test, basically, I took this library that we're talking about. And this, these are the, and it's only sort of a subset of the PHL. And so these are the minimum, maximum, and median retention time. And so I did two different things. So first of all, I took randomly added or subtracted up to ten Dalton's from every peptide. So maybe I added one and subtracted three and added ten and subtracted two. So basically it's randomized. And you can see that the minimum does go down by about ten. The maximum doesn't really go up and the median stays the same because I've done this randomly and so I've sort of added as much as I've subtracted. In this case, basically I took and did a fixed RT. So basically I said every peptide in here, I'm gonna add ten minutes. And then I'm gonna use this library for a swath analysis and I'm gonna see how the software can handle it. So between these two things, so this is sort of the baseline library. I've done a random thing where each individual change is probably less, but it's plus or minus. And in this case, I've added ten to everything. So everything in here is moved by ten minutes. So which one do you think gave the worst results? The one where I randomly added plus or minus, and the magnitude is probably averages around five. Or the one where I added ten to everything. Who thinks that the random one would be the worst? Who thinks the fixed one would be the worst? Who has no idea? Okay, no one's gonna play. Fixed one is the problem, that is correct. So basically this is a so-called whisker plot, box and whisker plot. The box and whisker plot basically, this is the median of your data. This is the first quartile, this is the third quartile. And this is the minimum and maximum. Although there is some outlier detection done and so sometimes you can actually get some things below the minimum or above the maximum. But basically it shows that the library that we started with has very narrow tolerance. I mean everything we're getting, so this is 15 different samples. We're seeing how many basically heel of peptides we're seeing. And in this case, each of our analyses came up with about 18,100, very tightly grouped. When we did these two retention time perturbations, we actually saw a significant decrease in not only the number that we see, but also the consistency across the different replicates that we see. So in a similar vein, basically we took the Q1 and Q3 values and we added basically modified by 40 ppm the Q1s or we modified by 40 ppm the Q3s. So this one, which would have more of an effect. We're taking these big Q1 chunks and then we're basically fragmenting them all and then analyzing the Q3 versus modifying the Q3, which is actually what we're reading out. Who thinks the Q1 will be a worse thing? Q3 will be worse. And that is exactly right. So the Q1, you're not really doing much. Maybe a couple of them, you're going to move it from one swath to another. But most of them are going to say in the same swath and so it doesn't really matter. You're just looking at basically the, you're looking at the same ions and it's still in the same swath. But in the case of the Q3, a change of 40 ppm again causes a drastic decrease in the number of peptides observed. Although it didn't affect as much the sort of reproducibility. So I'm going to talk about one sort of real world example. So basically we took a HeLa, do you guys know what HeLa cells are? They're a cell line, it's one of the oldest cell lines. It was taken from some poor woman back in the early, mid 1990s and was grown from a cancer. It was sort of the first cell line that became available and it's still in use today. And then we spiked in these halo peptides at different concentrations. And there's nothing special about the halo peptides, it's just a different organism than human. And so what we wanted to see is if we have this complicated background, can we see these halo peptides that we spiked in? So the five different dilutions and in the data I'm going to show, it goes from four femtomol to one nanomol. There's three replicates of each. Tested on nano and micro flow LC, two different instruments, interpreted with four different software tools, excuse me. So if you look at all the replicates, times machines and everything, there are actually 360 different measurements for each point. And so we basically took it and ran against the PHL and this is what we saw. So basically these are the two-fold, this is a log transformed, because when you have ratio data you always take the log. And ideally this would be right at two. And so what we've done is we've taken, and so this is sort of the two-fold. We're basically taking the ratio of everything to the most concentrated sample. So this E sample has the most things in it. And so we take the, and so pretty much anything in D is also going to be in E. And anything in C is also going to be in E. So this is most concentrated, less concentrated, less concentrated down here. So by the time we get to the very low femtomol sample we only see four or five, so actually the number that we see is here. So out of these 475 peptides we spiked in, we're only seeing 204. And actually this is peptide ions. And so there's going to be in excess of 500 possible things. And we're only seeing about half of them or really 40%. And so we looked at that and we thought, well that's not too good. I mean we have reasonable quantitation. I mean that everything was lining up on the, where it should on those axes. But we had poor agreement between all the replicates. So what we did is we looked at all the different experiments and we picked peptides that we're seeing in all three replicates of any one technique or software, what have you. And we created a subset database from this list. So basically the PHL had about 147,000 peptides. Our new database had 40,000 peptides. So what we've done is taken a repository library and we focused it on our sample. And so the reason for this is basically the way that people do big data nowadays. You take all these measurements and you don't try to threshold. You don't try to decide what's good. You don't try to take Excel and pick a cut off. What you do is you make some sort of statistical model and you try to separate the true positives from the negatives or the, yeah, anyway. So as you go here, as you push this way you get more and more sensitive. You get more and more things that you might not have gotten.  And so what you try to do is pick a point where you have an acceptable FDR. And the thing is with a big SWAT library, you don't expect to see everything in there. And so where all these things use decoys. And so you expect to have a one to one ratio of decoys to properly model this. But if you don't see 60% of your SWAT library and you make decoys for 100%, you basically have, basically you only have about 20% true forwards and about 80% decoys. So because you don't see everything in your library, having a big library in effect increases your number of decoys. And that is hard to model. And so by cutting that down, we hope that we'd have a better result. And it turned out that we did. So basically this is the same thing analyzed with the other library. And you can see that now we see in excess of 500 things, they're still pretty close. This is pretty close to minus two, this is pretty close to minus four. And we now see 23 of these lowest concentration ones. So I'll go back. I went from here to here. And so basically these lines along the bottom are a density plot. So kernel density basically gives you an idea of how these things are spread out. Because if you look at this cloud of things, it's kind of hard to tell. But you can see that these things are a little bit misshapen. And that's an indication that there's something a little bit weird about your data. This one has a pretty pronounced shoulder. And so sometimes what we do is we actually cut this one off at a CV, coefficient of variation of say 20%. So we exclude data that is problematic. But even by doing that, we get a much cleaner peak. And this density plot gets more nicely shaped. But we still have far more. So by using a smaller library, we've actually achieved, we've seen, we've done better quantitation on more peptides. And this is another way to look at the same thing. This is looking at just the Hela background. So these previous one, these are all the Hela peptides. This is looking only at the Hela background. And even in the Hela peptides, yeah, here we saw on average about 14,000. But here we saw over 16,000 on average. And as I said, sometimes this is max and min. But because they do outliers, sometimes you have outliers out here. So this is an indication that targeting your library. So we think that library resources are good. But you still have to do some focusing. It's good because you don't have to do all your own DDA. But it does require some customization. And I think that feeds in well with the proteogenomic theme. So SWATH is an important MS technique. It has the ability to be re-analyzed forever. You get better depth than DDA. And as long as you, since you can re-analyze forever, as our knowledge of the proteome space and our libraries improve, you're going to be able to re-analyze the same data and get better results. Library quality does matter. I really think that Docker is a useful thing, especially for somebody who's not that technically savvy. It's pretty easy to install.  And comprehensive resource libraries save time. You don't have to do your own DDA. But they should be tailored before use. And again, I think that leads into proteogenomics. Because what if you had some genomic data? And then you took one of these resource libraries and you said, OK, I think that in my genomic data, it tells me that I should see all these things. And so now you make a much more focused proteomics library. And you have a better chance of actually seeing what you're looking for. In today's lecture, you were introduced to the library assessment feature of SWATH Atlas, which provides recommendations to improve the DIA experiment. The DIA library QC workflow considers features such as library complexity, precursor, and fragment peptide characteristics, retention times, library completeness while assessing an ion library. We hope now you can appreciate the use of tools like a serum atlas, peptide atlas, and SWATH atlas in carrying high quality mass spectrometry-based proteomics research. Thank you.