Progenesis QI and the iKnife: the cutting edge of food monitoring

Dr Sara Stead, a Senior Strategic Collaborations Manager in the Food and Environment division at WatersEarlier this year at ASMS 2015, Waters previewed their Rapid Evaporative Ionisation Mass Spectrometry (“REIMS”) research system, incorporating the iKnife – an exciting new technology that’s already hitting the mainstream news headlines in the monitoring of food adulteration. Here at Nonlinear, we were incredibly proud to announce that Progenesis QI would provide the data analysis support, starting with Progenesis QI v2.1, which was released just last week.

In this article, we’ll talk with Dr Sara Stead, a Senior Strategic Collaborations Manager in the Food and Environment division at Waters, to learn more about the technology, its potential applications and how Progenesis QI helps.

Mal Ross: Hi Sara. Thanks for talking to us today. Can you start by telling us a little about your role at Waters, please?

Sara Stead: Thanks Mal. I’m based at the Waters mass spectrometry headquarters in Wilmslow, UK, and work within the Food and Environment market development group. I’ve been with Waters for 4 years and am responsible for strategy business development. Prior to joining, I worked at the Food and Environmental Research Agency (FERA) in York for 13 years as a senior scientist focusing on food safety, quality and integrity, gaining a lot of experience of the challenges associated with food testing, the industry needs and requirements.

At present, I’m working on the development of innovative solutions for the detection of food fraud & authenticity using MS-based techniques, including REIMS with iKnife technology.

Mal: OK, so I imagine you’ll have a strong appreciation of the benefits that a technology like REIMS can bring. First though, for those who’ve not heard, can you tell us a bit more about REIMS and the iKnife technology in particular?

Sara: REIMS with iKnife is certainly an interesting and innovative technology. REIMS is a new ionisation technique and the iKnife (Intelligent Knife) technology was originally developed for application in surgery, allowing surgeons to make real-time decisions during operations. A conventional electrosurgical generator and knife are used to generate gaseous molecular ions of the major tissue components – for example, phospholipids – via a diathermic process. The combination of surgical and MS techniques also offers a possibility for in-situ chemical analysis of tissue during surgery.

REIMS research system: iKnife and Waters Xevo G2-XS QTofREIMS offers a number of unique benefits that address the requirements of the food testing industry. One example is the direct sample analysis, which means results can be generated in near real-time, with minimal intervention. At the ASMS conference in June 2015, Waters made the technology available for research use and it’s currently available as a direct ionisation technique on the Xevo G2-XS QTof and Synapt G2-Si instruments. In combination with Progenesis QI, it’s possible to develop databases of chemical markers and generate MVA models allowing the real-time classification of unknown samples to be performed at the point of control.

Mal: Sounds great. I guess the really revolutionary thing here is the speed with which you can get results telling you exactly what you’re sampling? There’s no sample prep or chromatography step here?

Sara: That’s absolutely correct, Mal. Using the iKnife for sample introduction, there is no requirement for sample preparation, extraction or chromatographic separation, which are some of the major bottlenecks in the routine analysis of complex and diverse foodstuffs. The workflow’s greatly simplified, involving a few seconds’ “burning” of the analytical sample to generate an aerosol that’s then transferred to the MS using a pump mounted on the instrument. The use of Progenesis QI means you have a powerful multivariate statistics package to convert the MS raw data into meaningful results. And from here, you can develop databases of unique chemical markers, representative of different sample types.

Fish at market (photo courtesy of Lucas Jans)Mal: Can you give us an example of the type of analysis you’ve done using REIMS data in Progenesis QI? I imagine many people, in Europe at least, are quite familiar with the horsemeat adulteration that made the headlines last year, but I hear you’ve been doing something with fish too – is that right?

Sara: Yes, that’s right. I’ve been working on the development of a database using REIMS with iKnife and Progenesis QI for white fish speciation. Fish fraud’s thought to be one of the most widely perpetrated food frauds in the world. Estimates of the amount of fraudulent practice range from 25-75% depending on the geographic region and the species of fish involved.

Mal: Wow, that’s a lot!

Sara: Indeed! Species substitution is the most common type of fraud. This is where a higher value species e.g. cod is substituted by a lower value species e.g. whiting. It’s often used in situations where organoleptic identification may be difficult, e.g. processed foods.

So far, I’ve analysed samples of the most commonly sold white fish in UK shops using REIMS and the iKnife on the Xevo QTof. The data’s then been processed using Progenesis QI and EZinfo to develop unsupervised PCA and OPLS-DA models to separate the fish species based on their unique chemical profiles. The model can then be used to determine whether an unknown sample belongs to one of these species included in the model.

PCA plot of fish species samples in Progenesis QI v2.1

Mal: And is that as far as you’d go with this kind of application in Progenesis QI? Or would you also want to identify the molecular markers for the different species?

Sara: Oh, identifications are important too. It’s important to understand which chemical compounds are responsible for causing the differences observed in the MVA models so that we can assess both the quality and validity of the statistical models. We use the tools within Progenesis QI – such as database searching and tagging – to propose tentative identifications and generate marker libraries representative for the different fish species under investigation.

Mal: Excellent. So, I guess the applications we’ve seen so far are really just the tip of the iceberg. This kind of analysis sounds widely applicable and it seems REIMS in particular can revolutionise monitoring of the food supply chain.

Sara: Yes, REIMS technology is directly applicable to many areas of testing along the food supply chain – food authenticity, brand protection, food safety and quality, and nutritional analysis, for example. We also see applicability for the REIMS technology in areas such as environmental testing, sports doping and chemical materials analysis.

Mal: Exciting times, then! OK, thanks Sara – it’s been great talking to you. Hopefully, we’ll catch up with you again later to hear about more of the latest developments and success stories using REIMS and Progenesis QI.

Sara: Thanks for the opportunity to discuss the REIMS with iKnife work; definitely exciting times! From my prior experience in food analysis, I really believe we have a revolutionary technology platform here. It has the potential to evolve into a point-of-control analysis tool, operated in a field testing laboratory such as a border inspection post – it really could transform the way testing is performed! :)

If you want to see how Progenesis QI supports the analysis of REIMS data and other direct sample analysis techniques, you can download Progenesis QI v2.1 along with a quick-start guide that walks you through a small-scale version of the fish species study mentioned above. And for more information on the whole REIMS research system, visit the Waters website.

Progenesis QI v2.1 – available to download now

Back in March, we released Progenesis QI v2.0 and we’re pleased to bring you the news that v2.1 is now available to download. This point release brings further improvements to the identification process as well as a couple of other exciting new features.

What’s New?

  • Improvements to ChemSpider functionality with the option to perform theoretical fragmentation and filter your search results based on elemental composition
  • Integration with the NIST LC-MS MSMS libraries*
  • Integration with the IPA pathways tool from QIAGEN*
  • A new dedicated workflow for Direct Sample Analysis techniques such as REIMS, DESI (non-imaging), DART and LD-TD using a Waters mass spectrometer

*Integration comes as standard, but you must already have a licence for IPA and the NIST libraries are an extra cost option.

Where can I download it?

If you’re an existing customer with an up to date coverwise plan, you will receive an email with a direct download link. If you’re already using v2.0, there’s no need to upgrade your dongle to use this version. In addition, if your Progenesis PC is connected to the internet, there should be a message in the Experiments list sidebar notifying you of this new version – if you click this, and your dongle is plugged in, you’ll be sent to the download page:

Update panel in Progenesis QI

Please note this update will automatically overwrite any previous version currently installed.

If you’re thinking of trying Progenesis QI for the first time, you can download the software from here.

If you want to make use of the NIST libraries, please contact us and a member of our sales team will be happy to help.

How will I know how to get the most out of the new features?

We’ve expanded our FAQs to cover the new features, as well as updating any previously available FAQs to correctly reflect new behaviour.

MetSoc2015 – Bridging the gap between community and industry

At the end of June, I, along with some of my colleagues, headed across to San Francisco, CA, for Metabolomics 2015. This was my third time attending this conference so I was looking forward to seeing some old faces, as well as new ones. I was also curious to see whether the same hot topics from last year were still a focus.

We arrived before the conference was officially underway, so we took the opportunity to explore the busy city around us. Cycling across the Golden Gate Bridge wasn’t on my bucket list, but in hindsight I think it should have been; it was awesome.

The impressive Golden Gate BridgeAli cycling across the Golden Gate Bridge

As with other years, compound identification was a hot topic, and one of the first sessions of the conference was focussed on this area. Due to problems with the projector, the session began with an impromptu open discussion where people shared details on what libraries they were using, and what criteria they require before trusting an identification in a publication. We’ve recently added the option to search the ChemSpider libraries in Progenesis QI so it was good to hear ChemSpider is a popular choice. While ChemSpider proved popular, there’s still the issue of the huge number of possible identifications it can retrieve so it was great to be able to demonstrate the soon-to-be-released Progenesis QI v2.1 which allows filtering of ChemSpider searches using theoretical fragmentation.

Speaking of theoretical fragmentation, Dr. Steffan Neumann from the Leibbniz Institute of Plant Biochemistry, stated that “in-silico fragmentation is the next best thing if there is no reference spectra library around”. Steffan is head of the group that developed MetFrag, the basis for the theoretical fragmentation done in Progenesis QI – he was pleased with the work we’d done using this, and that the source code, with unit tests, is available on GitHub for the rest of the community.

MetFrag isn’t the only area where we’ve been working with the metabolomics community – we recently implemented the option to search LipidBlast, a computer-generated MS/MS database produced by the Metabolomics Fiehn Lab. Progenesis QI v2.1 will also include support for the NIST MS/MS libraries. Of course, as well as using tools developed by community projects, we also recently released Progenesis SDF Studio v1.0, a free compound database management tool – just one of our ways of saying “thank you”. In other industries it’s quite common for commercial organisations and community projects to work together for software development, so it’s great that the metabolomics world is starting to see the benefits of this, and I’m very pleased to be a part of it.

There was a great turn out for the talksAli, Jon and Mark busy on the Nonlinear booth

If you’re working on a project you would like to integrate with Progenesis QI, get in touch – we’d love to hear from you.

Progenesis SDF Studio v1.0: using MOL files just got easier

Back in April, we released the Early Access Edition of the free tool Progenesis SDF Studio and we’re pleased to announce that v1.0 is now available to download.

Editing with syntax highlighting

What’s New?

We’ve been busy listening to your feedback on v0.9, as well as fixing reported bugs, to implement the most popularly requested improvements, with a focus on simplifying the process of fixing invalid records:

  • Line numbering – each line is now numbered so locating reported errors is much easier
  • Syntax highlighting – easier to differentiate between different fields
  • Automatic underlining of each error
  • Improved error messages
  • Improvements to editing compound structure – fields are now highlighted and tooltips indicate each field’s function
  • Improved support for ChemSpider MOL files
  • Bug fix: edits to URL and Description are now saved
  • Other minor bug fixes

How do I get it?

If you’re not already using Progenesis SDF Studio, you can get it free from our download page. If you’re one of our early birds and are already using v0.9, you can click on the message in the software’s web panel telling you to update:

Updgrade panel (arrow)

How do I use it?

We’ve designed Progenesis SDF Studio to be as simple as possible, so hopefully you won’t need much assistance. That being said, we’ve updated our FAQs and you can also contact us if your question isn’t covered there.

How can I suggest further improvements?

Just as with our LC-MS analysis software, we’re looking to continuously improve and develop Progenesis SDF Studio, and for that we need your input. If you’ve got some ideas on what you’d like to see implemented or improved, let us know.

ASMS 2015: Mass specs, plugs and rock ‘n’ roll

Vicki Elliff and her giant colleague, Brad, at ASMS 2015 “Progenesis QI – for small AND large molecules”

Just over 3 weeks ago now, I set off on the first of 3 flights to travel from Newcastle-upon-Tyne, UK, all the way to St. Louis, MO, for ASMS 2015. This was my first overseas trip for Nonlinear, so I was both nervous and excited for the week ahead. We arrived on the Friday evening (which felt more like Saturday morning due to the time difference!) so it was more or less straight to bed ready for our bright and early start at the Waters Users’ Meeting the following morning.

The users’ meeting kicked off with breakfast and a chance to mingle before an exciting introductory talk about what’s new from Waters – this included the unveiling of their new mass spec, the Vion IMS QTof, a preview of REIMS research system with the iKnife, and also the launch of v2.1 of Progenesis QI (more on this below). This preceded the 2 key note presentations, both of which discussed applications of the iKnife. The first talk was by Professor Zoltan Takats from Imperial College London, the pioneer behind the iKnife – he gave us a very emotive overview of how it could help to prevent surgical removal of healthy tissue, with the example of full mastectomies in the case of breast cancer, as well as reducing time spent on the operating table waiting for histology results. With an estimated 1 in 3 people developing cancer at some point in their lifetime, this was a poignant talk showing a real life benefit of a new technology.

Next up was Chris Elliott from Queen’s University Belfast – his talk was on the very different, but nevertheless important, topic of food fraud. Food fraud is something that has received a lot of media attention over the last few years, from the melamine milk scandal in China, to the horse meat adulteration in Europe so it was great to see that the science industry is coming up with new and innovative ways to tackle these issues, and perhaps more importantly, that the wider world is beginning to see the importance of more stringent testing and regulations. Chris gave a very enlightening talk about how big the problem really is, and how it’s not just limited to these headline grabbing stories; one such example is about how twice as much organic food is sold as is manufactured. Some serious “food for thought” just as we finished for lunch.

After lunch, we split into groups of different areas of interest, although there did seem to be a theme that was consistent across them all: the use of Progenesis QI for the data analysis. There was a certain sense of pride at seeing how well represented we were, and also at how far we’ve come since our acquisition by Waters. This was a good taster of what was to come for the week ahead.

Sunday was a chance for us to explore a bit of what St. Louis had to offer, specifically the zoo which is located inside the enormous Forest Park. Personal highlights included the sea lion exhibit where you walked through a glass  tunnel with them swimming over you, and also the sight of a sleeping chimp right up against the glass.

Sea lion at the St Louis ZooA pensive chimp at the St Louis ZooSeal at the St Louis Zoo

On the Monday morning, the hospitality suites opened, which was where my Nonlinear colleagues and I were based for the duration of the conference, delivering software demos and also answering whatever questions were thrown at us from both new and experienced users. In addition to demos and answering questions, we received loads of great suggestions of what we could do next, and also heard about novel applications for which people are already using Progenesis.

As mentioned earlier, ASMS was our first opportunity to demo the soon to be released v2.1 of Progenesis QI. If you weren’t lucky enough to hear about it then, here’s your chance to see what’s coming:

  • Integration with the NIST MSMS libraries
  • Improvements to ChemSpider functionality with the option to filter your search results based on fragmentation data and elemental composition
  • Integration with the IPA pathways tool from QIAGEN

Dr Ian Morns demonstrating Progenesis QI at ASMS 2015We were more or less fully booked for appointments during the daytime sessions, even having to take an extra PC station to keep up with demand, and with Progenesis featuring on a high number of posters this year, word was getting around about us which meant all hands were on deck for the evenings when the suite was open to all. The evening sessions were slightly more relaxed – even if they were no less busy – with 80’s rock blaring in the background, and flashing neon guitar necklaces hanging off everyone’s necks to fit with Waters’ “Science is my rock ‘n’ roll” theme. The atmosphere was buzzing, drinks were flowing, and we were glowing with pride at how complimentary everyone was about the software – a particular favourite seemed to be the new Progenesis SDF Studio; after all, we all love a freebie!

Our breakfast seminar was on Wednesday morning, with talks on metabolomics and proteomics by Geert Goeminne, Ghent University, VIB Department of Plant Systems Biology and Richard Sprenger, Department of Biochemistry and Molecular Biology, University of Southern Denmark, respectively. I’m pleased to say we had a great turnout, with standing room only. The seminar was recorded, so keep an eye on our Twitter for details.

The Progenesis QI breakfast seminar at ASMS 2015Dr Richard Sprenger presenting at the Progenesis QI breakfast seminar, ASMS 2015

After a hectic, but enjoyable, few days, we started our journey home with freshly inflated egos – it’s a good feeling knowing that we’re on the winning team.

Strong technical support: a founding principle of Progenesis QI

Everyone can tell a personal tale of poor customer service that they’ve experienced, but here at Nonlinear, we’d like to think that none of those tales will involve us. We take support very seriously indeed, so it’s nice to hear that many of you appreciate the efforts we put into making your use of Progenesis as rewarding an experience as it can be.

Just recently, we’ve added a selection of customer quotes to our website that let you see for yourself that when you buy Progenesis QI, you’re not just getting some software to install – you’re also getting the benefit of our support team’s many, many years of data analysis experience. And you can rest assured that you’ll be supported promptly – something that can’t be said for all software.

Here are just a few examples of what people are saying…

“Technical support is fast and has been very helpful”

“We have been using the new version of Progenesis QI for proteomics to analyze a complex set of samples from an ambitious experiment. New users have got familiar with the application very quickly and have had the opportunity to try different protocols and experimental designs fairly easily. It is user friendly and allows you to go back and forth through the workflow and to clearly visualize the results.

“Moreover, the technical support is fast and has been very helpful every time we needed it. The attention provided by the technical staff from Nonlinear was an added value of Progenesis from the beginning.”

Prof. José Antonio Bárcena
University of Córdoba, Spain

“User-friendly and intuitive and the technical support is great”

“In just a short period of time, Progenesis QI for proteomics has become a key software tool in our data analysis platform. We use it for quick quality checks of our data as well as for complete, integrated label-free quantitative analyses. Its strengths include the accuracy of the alignment algorithm, the highly appreciated QC metrics section and the availability of the multivariate statistics tools. Moreover, it is very user-friendly and intuitive and the technical support is great. A must if you go for label-free!”

Elisabeth Govaert, PhD student
Laboratory of Pharmaceutical Biotechnology, Ghent University, Belgium

“As usual, Nonlinear provided wonderful technical support”

“To our surprise, with Progenesis QI for proteomics we practically started getting publishable data within the first few hours. We started writing the paper, while doing more experiments to confirm the quantitation. In 4 weeks, our paper was written! As usual, Nonlinear provided wonderful technical support for us.”

Dr. Lam Yun Wah
Department of Biology and Chemistry, City University of Hong Kong, China

“A prompt response to everything”

“We like Progenesis because it allows us to separate quantification from identification which lets us build complex workflows, it is easy to use which is important in our academic lab, it is very sensitive to finding features of interest, the license system works very well such that we can install Progenesis on many PCs without restriction, and it is easy to use.

“We have worked very well with the Progenesis team for more than 7 years and have great support in terms of prompt response to everything from simple questions to complex features requests.”

Prof. Mark E. McComb
Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA

If your support contract is coming to an end, has already ended, or you simply want to extend your contract early to make sure you have continuous cover, get in touch now. And remember, every annual support contract comes with a further year of free upgrades. What’s not to like?! :)

Come and see us at ASMS 2015!

They say time flies when you’re having fun, so that must explain how it’s already time for ASMS 2015 – the  63rd annual conference for the American Society of Mass Spectrometry. This year it’s being held in St. Louis, MO, in America’s Center Convention Complex, with hospitality suites in the nearby Renaissance Grand Hotel. The conference starts officially on Sunday 31st May and runs until Thursday 4th June, which gives you plenty of time to come and see us for a chat about how Progenesis QI can (or already is) helping you with your ‘omics data analysis. We’ll be attending alongside our colleagues at Waters again this year, so come by to either booth #160 or the Waters hospitality suite, located at the Renaissance Grand Hotel.

So, what have we got planned for this year?

Announcement of v2.1 of Progenesis QI

We’ll be confirming what’s coming next for Progenesis QI with the opportunity to book a demo to see these new features for yourself. If you’re not able to attend ASMS this year, don’t worry – we’ll be posting full details of this release after the announcement and you can still send us an email to arrange your own demo.

Breakfast Seminar

We’re hosting a breakfast seminar on the Wednesday morning from 7-8am with talks from Geert Goeminne, Ghent University, VIB Department of Plant Systems Biology and Richard Remko Sprenger, Department of Biochemistry and Molecular Biology, University of Southern Denmark. Please note that pre-registration is required to attend this event, so please register now to avoid disappointment.

Software demos

We’ll be taking bookings for software demos in the suite, so just pop along to the suite (or the booth) to reserve your slot. In addition to demonstrating the software, you’ll have the chance to meet with some of our development team to get your questions answered. Please note bookings are required during the day, but the suite is open to all from 8-11pm Monday – Wednesday which is when we’ll also be giving out some exciting freebies.

In addition to the above, I’m also very excited to confirm Progenesis QI features in a number of posters that will be presented this year so keep an eye out for those.

Hopefully we will see you very soon. Smile

Spectral counting: why not?

One of the key considerations in bottom-up label-free proteomics analysis is the means of feature quantitation. Being peptide ions, measurements of these features are ‘rolled up’ into inferred proteins, but two main approaches can be taken to generating the data for this purpose.

The first, and most commonly used, approach is MS1 (precursor-based) measurement such as calculating the area under the MS peak for the feature, or the height (maximum intensity) of the peak. The former is the method used by Progenesis QI for Proteomics. These readings can then be summed for all the features comprising inferred proteins.

The second approach is MS2 (product/fragment-based) measurement. Prominent among this type of method, in Data-Dependent-Analysis (DDA) experiments, is quantitating a protein by summing the number of identified MS2 spectra derived from and matched against its peptides. This approach is known as spectral counting. The value obtained will depend on the intensity of the protein’s precursor peptide ions, as in DDA analyses more abundant features will be sampled more often than lower abundance ones.

Good reviews of these approaches in the wider context of MS-based quantitation as a whole are available (for example, [1-3]).

Why don’t we use spectral counting?

We are often asked about spectral counting by customers. It is an easy-to-apply and convenient method for relative quantitation purposes, for which the same process required to identify the proteins present in the sample also provides the quantitative data. It also allows a comparison to be made between very different samples, by reducing the comparison to the identification level. However, it is not an approach we employ within our software workflow, because of i) deficiencies in the method for quantitation, and ii) the assumptions upon which it is based running contrary to our approach.

i) Quantitative performance

Fundamentally, MS1-based measurements are more accurate and precise than spectral counting with a better linear dynamic range. This arises due to a number of weaknesses of spectral counting:

  • There is no direct measurement of peptide ion properties inherent to the approach, discarding potentially important characteristics of a peak.
  • The response in terms of spectra per peptide ion is not constant across different features.
  • Measurements can also be affected by the level of competition with other features for DDA selection, which may vary within and across samples.
  • The linear dynamic range of the method can be limited by saturation effects.
  • There is a stochastic aspect to DDA sampling, hampering reproducibility; DDA sampling is also biased towards more abundant species, for this reason.
  • Dynamic exclusion methods, designed to improve DDA coverage, can also affect the response.
  • Any changes to the base MS2 sampling conditions between runs will prevent inter-run comparisons.
  • It is problematic to deal with the complication of peptide ions being shared between proteins, and assigning counts appropriately.

For these (and yet more!) reasons, spectral counting is particularly weak at robustly estimating low fold changes in peptides between samples, and requires a large number of spectra per feature to be reasonably accurate; it could be considered a semi-quantitative technique, and with our focus on robust accuracy, we did not feel that it was suitable for inclusion as a quantitation method in our software.

There have been a number of efforts to improve the effectiveness of spectral counting for quantitation, and variations on the approach. These include normalisation of the counts to various parameters, and the development of more complex indices such as emPAI [4] and APEX [5]. An element of direct quantitation can also be introduced by measuring the intensities of the fragment ions themselves for spectra assigned to a given feature [6]. It is fair to say that MS2-based methods can perform reasonably well for relative quantitation, albeit not as well as MS1-based methods (e.g. [7,8]) and we certainly don’t dismiss them out of hand. However, there are crucial and fundamental limitations to spectral counting analysis, which discards a great deal of quantitative information from the run.

ii) The involvement of identification in quantitation

Spectral counting uses identification and assignment of spectra as its basic measurement. This also carries several weaknesses. For one, the measurements are not only affected by ‘experimental’ factors such as instrumentation settings, but also subject to variation in the identification process. Results are contingent upon external identification databases, their curation, and the search settings, introducing extra dependencies into the quantitative side of the analysis. This would affect the benefits of our quantify-then-identify approach, in which we identify only after extracting maximum information from the raw data for optimal normalisation and multivariate visualisations.

More drastically, unidentified features simply cannot be quantified. This would prevent any identification-free classification, normalisation, or QC approaches – three areas where this really does matter.

Quantifying first is much more future-proof. Identifications may always be added to unknown, but fully quantified features of interest in an MS1 map via later targeted runs; you can’t add quantitative results to unidentified features in spectral counting.

Finally, one of the challenges commonly ascribed to MS1-based approaches is that valid MS1 quantitation requires accurate alignment of precursor features between complex runs, given that the process is not ID-driven. However, this is achievable, and we provide means by which you can overcome this challenge; there is no restriction to driving cross-run comparisons via identification-level matching. Instead, we can truly compare each precursor feature directly using like-for-like measurements.

Given all this, can I still get spectral counts from Progenesis QI for Proteomics?

Of course! We do understand that some users may wish to obtain spectral counts from their data, and it’s never been our policy to deny you data that may be of use to you. Because of this, we do allow the export of spectral counts for your own ends. If you wish, you can then perform your own analyses using MS2-based approaches.

To obtain these data, follow the instructions in our FAQ on the topic of data export. You can obtain the spectral counts at the protein level using the instructions under “Protein Data”.


[1] Bantscheff M. et al. (2007). “Quantitative mass spectrometry in proteomics: a critical review”. Anal Bioanal Chem 389(4):1017–1031 (Open access).

[2] Bantscheff M. et al. (2012). “Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present”. Anal Bioanal Chem 404(4):939-65.

[3] Soderblom E.J., Thompson J.W. and Moseley M.A. (2014). “Overview and Implementation of Mass Spectrometry-Based Label-Free Quantitative Proteomics”. Chapter 6, pages 131-53 in: Quantitative Proteomics, Issue 1 of “New Developments in Mass Spectrometry Series”. Editors: Eyers C.E and Gaskell S.J., Publisher: Royal Society of Chemistry, ISSN: 2044-253X, ISBN: 9781849738088.

[4] Ishihama Y. et al. (2005). “Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein”. Mol Cell Proteomics 4(9):1265-72 (Open access).

[5] Braisted J.C. et al. (2008). “The APEX Quantitative Proteomics Tool: generating protein quantitation estimates from LC-MS/MS proteomics results”. BMC Bioinformatics 9:529 (Open access).

[6] Griffin N.M. et al. (2010). “Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis”. Nat Biotechnol 28(1):83-9 (Open access for linked PMC version).

[7] Grossman J. et al. (2010). “Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods”. J Proteomics 73(9):1740-6.

[8] Krey J.F. et al. (2014). “Accurate label-free protein quantitation with high- and low-resolution mass spectrometers”. J Proteome Res 13(2):1034-44 (Open access for linked PMC version).

Q&A: Elemental Composition in Progenesis QI, with Dr Jayne Kirk

Photo of Dr Jayne KirkLast month, we released version 2.0 of Progenesis QI, with a number of improvements in its compound identification workflow. One of these new features was the ability to calculate a compound’s elemental composition.

Here, we’ll interview Dr Jayne Kirk, a Senior Applications Chemist at Waters, to learn a little more about the feature and how it can help your small molecule analysis.

Mal Ross: Hi Jayne. Thanks for talking to us. Can you start by telling us a little about your job and the type of analyses that you perform, please?

Jayne Kirk: Hi Mal, I work in the Applications Laboratory in Wilmslow, UK, and have been working on metabolomic and lipidomic applications for 8 years now. Before joining Waters, I completed my PhD at York University, UK, in Chemistry.

My role in the laboratory is to perform small molecule demonstrations for clients from all over Europe, provide training and also to offer support to our MS specialists. Last year plant metabolomics (my personal favourite) was a hot topic, whereas this year lipidomics requests are flooding in!

Mal: So, we’re here to talk about how calculating elemental composition can help your compound identification. That ability is new in Progenesis QI v2.0, but how does it work? How much control do you have over the composition?

Jayne: A QToF Mass Spectrometer provides accurate mass information. Data processing within Progenesis QI generates a list of markers with m/z, retention time (and collisional cross section) information. After acquisition and processing, identification of markers is the next step. The elemental composition calculator allows assignment of a molecular formula to those markers.

The tool within Progenesis QI gives full control over the elements and the number of elements included in the search. It’s also possible to set and save several ‘typical’ search parameters for different classes of compounds, making the process very efficient.

The Elemental Composition parameters dialog in Progenesis QI v2.0

Mal: OK, so when should I use this feature? Don’t I already get this information in the IDs returned by my compound database searches?

Jayne: There can be times when your markers may not match anything in your compound database; in these cases, it’s necessary to go to the elemental composition calculator.

Mal: So, how do you typically use the calculation of elemental composition in your own small molecule analysis?

Jayne: Elemental composition is a building block or another piece of the puzzle and without that piece of information, it’s impossible to complete the jigsaw. Getting the elemental composition, whether it’s from the calculator or database searching, is essential.

It might not be necessary (depending on the experiment) to assign an elemental composition to all of the markers, however; instead, you can use the statistical tools to determine the important markers in the metabolomic or lipidomic study. Identification of these key markers is really the critical part of the process and if no database hit is returned, a molecular formula can still be obtained, giving you a starting point for further investigation.

Integration with ChemSpider, for instance, is another new feature within Progenesis QI v2.0 and another great building block. Here, the workflow would be to perform a ChemSpider search on the markers by mass and then filter that list of hits based on the elemental composition. Depending on the application area, certain elements are going to be of more interest in the search than others, so this is a way of filtering that information appropriately.

It’s great that you’re incorporating so many tools like this, helping scientists like myself to investigate, characterise and identify the markers in what are increasingly complex experiments.

Mal: We try our best!

So, rounding off, is this something you’d recommend to most people using Progenesis QI?

Jayne: Most definitely, yes. It’s another tool in the box which can be used in combination with the isotopic match, databases and pathway options within Progenesis QI.

Mal: Thanks, Jayne. It was great talking to you.

If you want to take advantage of the support for calculating elemental composition, as well as ChemSpider, LipidBlast and pathways integration, why not download Progenesis QI today and try it out?

Wall to wall proteomics in Berlin

A few weeks ago, I attended the Proteomic Forum in Berlin, which was held in The Technical University, from 22nd to 25th March. It was my first time in Berlin, a cosmopolitan city with a fascinating mix of people where, just as in London, anything can happen. :) Since it was my first visit to Berlin, it was also the first time I attended this event, and a great opportunity for me to meet with German scientists and my Waters colleagues based in Germany.

As usual, the interesting content of the program kept me busy all day long, but I had the opportunity to do some sightseeing during the evenings: from the Brandenburg Gate to Potsdamer Platz, an entire quarter built from scratch since 1995, after the Wall came down.


The program was rich and diverse, with discussions on a range of approaches from top-down proteomics to imaging techniques, but common themes across the varying approaches were the importance of PTMs and pathway analysis. Pathway analysis is actually one of the areas we focused on with the release of the latest version of Progenesis QI for Proteomics, helping scientists to understand the biological context of their results. For instance, with the pathway tool IMPaLA, which is directly supported by Progenesis, you can go further and get a biological interpretation of your quantitative results.


IMPaLA can also easily merge results from a proteomics experiment and a metabolomics experiment, so this functionality is also available in our software for small molecules, Progenesis QI. I had the opportunity to demonstrate this at the Gen2Bio conference, a regional metabolomics meeting held in La Baule, Western France, just after the proteomic forum.

If you want to know more about the latest releases of Progenesis QI or Progenesis QI for proteomics, or want to try it with your own data, please get in touch. If you’d like the opportunity to catch up with us in person at a future event, keep an eye on our events page to see where we’re headed over the next few months.