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by David.Chiang@SageNResearch.com

Proteomics technology is now a robust discovery tool, at least in capable hands with the right tools, for characterizing post-translational modifications such as phosphorylation, right alongside gene expression and cellular imaging for tumor and stem cell research.

However, the complexity, scale, and criticality of the data from a modern mass spectrometer such as an Orbitrap Velos are well beyond the capability of desktop PCs and require specialized infrastructure IT solutions.

When losing data becomes catastrophic rather than merely annoying, it is time to move beyond PCs into robust infrastructure solutions, such Sage-N Research’s SORCERER Enterprise system. Unlike traditional business-oriented IT systems, the SORCERER Enterprise system is optimized for the large multi-gigabyte data files of proteomics research.

Robust servers and storage systems provide the needed capacity, reliability, and throughput for storing and analyzing proteomics mass spec data that inexpensive PCs cannot provide. For example, a typical throughput of 300GB of raw data per week for a single mass spec will fill up a PC in less than a month. As well, the lower grade disk drives used in cost-sensitive, consumer-oriented PCs and external USB drives can lead to costly data loss and system downtime.

In addition, the nature of the data analysis needed for proteomics is changing, as it becomes more akin to hedge fund data mining than an administrative assistant running an Excel spreadsheet. This is especially true for quantitation and ETD data analyses where the field has not settled onto a de facto one-size-fits-all methodology, and where some semi-customization of the analysis to query and adapt to a particular data-set will be necessary. This is why the large-scale SILAC papers are always done by research groups with their own bioinformatics resource, and why just about any off-the-shelf software you can download or buy will probably not work well for your needs without some customization.

Why does quantitation or ETD software need to be semi-customized? Read the rest of this entry »

As you may know, Sage-N Research offers three SORCERER platforms — the SORCERER Enterprise, the SORCERER 2, and the SORCERER Lab.

The SORCERER Enterprise
The SORCERER Enterprise is a customizable and secure throughput and biorepository system for aggregate analysis. Provided as a scalable Blade server with integrated life-science optimized storage, the Enterprise system handles up to a few terrabytes of data and is highly scalable using additional computing resources. This platform is ideal for labs that are highly productive or focused on generating continuous high-throughput data, and can analyze 100,000+ spectra/hour — even those with post-translational modifications.

The SORCERER 2
The SORCERER 2 is a mainstream product for most proteomic labs — those with frequent but not continuous high-throughput needs. It is well-suited for modern instruments like the Thermo LTQ and Orbitrap, ABI 4700 and 4800, and Waters SYNAPT G2 and handles 2+ MS spectra/second, or 30,000+ spectra/hour. This system is a stand-alone platform and not scalable like the SORCERER Enterprise.

The SORCERER Lab
The SORCERER Lab is a lower-cost, entry system that is simple, lightweight, and compact. Designed to plug-and-play and require low IT maintenance, it contains the most essential yet basic capabilities, including SEQUEST 3G, TPP, and Scaffold. The SORCERER Lab is still more powerful compared to other PC-based systems. At 10,000+ spectra/hour, it has one-third the analytical throughput of the Discovery system.

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Starting with v4.0 software, the Sage-N Research SORCERER platform will provide the 2-stage scoring (i.e. different from 2-stage searching) architecture that generally mimics the current Gygi Lab workflow, which does a first-stage SEQUEST (i.e. SEQUEST 3G starting with v4.0) followed by our open-source MUSE scripting version of the Gygi Lab’s “Bino 5-score”. (This is analogous to the Mann Lab workflow, which generally uses a Mascot first-stage followed by a “6-score” re-score stage, according to private communication with Matthias.)

Users can also modify these re-score modules to incorporate their own scoring functions, such as to accommodate water and/or ammonia losses, incorporate special cleavage rules, or otherwise tune coefficients and parameters.

Anything to keep in mind about Probability Scoring?
Some researchers mistakenly believe that a “probability” is some kind of absolute “word of God” but they are very much a creation of man. Indeed, in science, a probability of an event has more to do with you — or rather your lack of all the relevant information — than the event itself, and is best considered a “degree of confidence” measure based on incomplete information. After all, mass spectrometers do not measure peptide sequence per se, but only a collection of mass/charge ratios from which you infer sequence information.

Probability Scores are simply tools that based on underlying (sometimes hidden) models, which as George Box observed are always “wrong” because they necessarily involve simplifications and assumptions. Probability Scoring, by its nature, tends to have increased specificity but reduced sensitivity. Their Achilles heel is the filtering step - how does one decide which peaks are “real” and which are “noise”, particularly for noisy spectra common for phospho and low abundance peptides? With only a handful of matching peaks to determine the Score, their accurate selection becomes critical.

Therefore, they are best used as a second re-scoring stage of results from a search engine like SEQUEST 3G designed to find specific patterns with significant noise. In addition, it is important to note that p-values are NOT true probabilities, since there is no requirement for such values of competing hypotheses to sum to 1. (See this Proteomics 2.0 blog entry for further discussion: http://proteomics2.com/?p=65 )

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by David.Chiang@SageNResearch.com

First off, I may need to apologize to those who take offense at the equivalent of someone trying to lift spirits at a funeral, as I am not trying to make light of the seriousness of today’s challenging economic circumstances.

However, I subscribe to the philosophy of author Anthony Robbins and others that there is always a positive to any negative, and that a proper mindset is key to move yourself forward, no matter what life throws at you. If life gives you lemons, it’s an opportunity to build a lemonade business empire.

Today, it is more important than ever to focus one’s mind on a positive path forward, because quite honestly, there are signs that the post-recession recovery could well be the opportunity of a lifetime for many of you!

It may seem perverse to have such a view given the prevalence of all the bad news, but history is on my side.

In fact, for those of you relatively early in your career, with at least 10 to 20 good working years ahead of you, I believe the career gods may well be smiling on you, as you have the best chances of catching the wave of the upcoming Biotech Revolution 2.0 — the one centered around proteins rather than DNA or cDNA.

Let me explain why this is so, and what you must know to win big in the next decades.

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President Obama unveiled a stimulus package in February that includes about $10B funding for NIH over two years. He specifically called for cancer research, which will get about $1.26B. In March, he will lift federal funding restrictions for stem cells. Other countries may follow suit. Since cancer and stem cell research make up more than 2/3 of advanced proteomics research today, this is very good news for proteomics!

Stimulus grants are likely one-time grants, so it should be viewed as a start-up grant for building up or completing your advanced research capability. In particular, focus on tools that increase automation and reduce manual intervention, including any tech support and maintenance that can improve your research productivity over the next 3 years.

For advanced “Proteomics 2.0″ analyses capable of large-scale analysis of important PTMs (phosphorylation and ubiquination), you would need (1) one or two high-throughput mass-accurate mass spectrometers, (2) a high-throughput software workflow capable of sensitive PTM analysis, (3) a robust compute server and storage system, and (4) several years of software and hardware warranty and maintenance.

For example, this is a proven basic setup suitable for advanced phospho-proteomics for cancer and stem cell research:

1) LTQ-Orbitrap mass spec
2) SORCERER 2 integrated data appliance
3) SORCERER ISIS-10 storage system with 10 terabytes
4) Recommended optional software on PC: Proteome Discoverer, Scaffold
5) Recommended optional software on SORCERER: Mascot, Phenyx

The SORCERER 2 IDA system includes a high-throughput SEQUEST and two integrated high-throughput workflows (Scaffold Batch and Trans-Proteomic Pipeline), as well as specific tools for phosphorylation and an integrated scripting environment for workflow customization. The SORCERER ISIS storage subsystem works directly with the SORCERER IDA to provide sufficient secure storage for several years of typical throughput. They both share the same warranty for 3 years, simplifying the IT maintenance.

A more advanced system, particularly for statistically robust biomarker discovery, including isotope labelled quantitation (iTRAQ), is the following:

1) LTQ-Orbitrap with HPLC
2) MALDI-TOF/TOF mass spec (e.g. ABI 4800)
3) SORCERER 2 integrated data appliance
4) SORCERER ISIS-20 storage system with 20 terabytes
5) Recommended optional software on PC: Proteome Discoverer, Scaffold
6) Recommended optional software on SORCERER: Mascot, Phenyx

In most cases, Sage-N Research can assemble the entire data analysis system with the noted tools pre-installed and pre-configured as a plug-and-play system with unified warranty.

Not surprisingly, what we recommend coincides with our own product portfolio. Undoubtedly, some would think that we are simply recommending what we sell.

Actually, quite the opposite is true — we sell what we would recommend. As the only prominent search engine provider that doesn’t promote our own proprietary search algorithm (we resell SEQUEST, Phenyx, and X!Tandem inside SORCERER, and would pre-install Mascot on request), we are free to pick and choose the best-of-class software and hardware components to deliver the most robust, sensitive workflow systems.

Advanced proteomics holds great promise, especially for cancer and stem cell research. Unfortunately, six years after Scott Patterson proclaimed in Nature Biotechnology that data analysis is proteomics’ Achilles heel, it is still true. The fact is, there is no way you can realize the full potential of an Orbitrap for advanced proteomics using just a PC.

Please contact me personally to see if we can help. The best way is to send me an email at: david@SageNResearch.com. Together, we can realize the full potential of proteomics to benefit everyone.

To see and hear what some of our SORCERER clients have to say about their own experiences, just click the link below:

Click Here for Video of Dr. Rich James (Randall Moon Lab, University of Washington, WA, US)

There is a continuing market shift toward “appliances” (application-specific systems) and away from software and hardware.

During this last week, both Microsoft and Intel have announced rare layoffs.

So who is doing well?

Apple (nasdaq:AAPL), for one, experienced unexpectedly strong financial results:  http://blogs.zdnet.com/BTL/?p=11563 .

Its sales are increasingly dominated by its iPod and iPhone appliances — computers that are tuned for one application for increased usability and reliability.

Network Appliance (nasdaq:NTAP) for another. NetApp sells storage appliances that are servers configured only for maintaining a large file system. Its products are also tuned for one application for usability and reliability. NetApp beat out Google as the top place to work in Fortune Magazine’s survey:    http://www.siliconvalley.com/opinion/ci_11529119

Why should you in proteomics research care?

Because data analysis continues to be the Achilles Heel of proteomics (see Scott Patterson’s Nature Biotech 2003 article), and IT trends determine the optimal value proposition comprising hardware and software systems.

The reason for the shift toward appliances is because of the changing cost dynamics.

Twenty years ago, you would buy $500 software for your $5K computer, so you need to have general-purpose computers to handle multiple software applications.

Today, it’s the reverse: you are more likely to buy $5K software for your $500 computer. Therefore, it makes less sense to re-use hardware for cost reasons alone, especially if it compromises application usability.

I think it is amazing that a high-end iPod costs more than a low-end Dell PC with monitor! Such is the case when the value is in the application, not the hardware.

Therefore, we expect that advanced proteomics analysis — where your server may see 80%+ usage — may similarly be best served by a dedicated analysis appliance, such as the SORCERER integrated data appliance, for improved usability and reliability.

Common PC proteomic software is designed primarily to be easy to use with low throughput and small datasets up to a few 1000 spectra. PC programs like Mascot or other software generally work fine at this scale.

However, high-throughput and large-scale analysis (e.g. 100K+ spectra experiments) — a foundation capability for biomarker discovery, molecular profiling and advanced post-translational modification research, requires a different methodology because of the increased need for sensitivity, noise-reduction, and automation.

Horses for Courses

This British maxim states that what may be suitable for one situation may not be suitable for another, as no one race horse is ideal for all course conditions.

When you need to go somewhere, you would walk, drive, or take a plane depending on whether the distance is 1, 100, or 10000 miles/kilometers, respectively.

If your annual income is USD $1K, $100K, or $10M, you would prepare your tax forms manually, use the TurboTax software, or hire a very expensive accountant, respectively.

However, I still occasionally meet scientists who mistakenly believe they can evaluate a large-scale workflow by using a simple BSA or other standard commercial mixture.

Advanced, large-scale analysis is highly specialized, and requires a lot of messy statistics tested against big datasets for true validation. Unless you enjoy that sort of thing, it’s easier to find someone else you respect who has done the heavy statistical lifting for you, so you can focus on what’s really important for you.

Two common large-scale workflows, both use SEQUEST

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by David.Chiang@SageNResearch.com

In the classic A Tale of Two Cities, Charles Dickens wrote the famous line, “It was the best of times, it was the worst of times …”

This is an accurate description for these extraordinary times. It has been very difficult for those among our friends and families who suffered losses in jobs, housing, and retirement accounts. With things likely to get worse before getting better, these are indeed the worst of times in recent memory.

However, it is important to keep in mind that extraordinary times breed extraordinary opportunities. Many great inventions and companies were created or forged during deep recessions. If history is any indication, these will also turn out to be the best of times, at least for those who can plan and act strategically.

In the middle of a tsunami, whether oceanic or financial, there is not much one can do but to try to hang on and not get swept away. Afterward though, the sea level returns to normal and renewal begins, eventually leaving everything better and fundamentally stronger that it once was.

Looking at the positive side of the global correction, the pendulum will likely swing back toward substance (particularly medical research and technology) and away from fluff. It would be refreshing for the world to value drug discovery and stem cell research on par with YouTube and Facebook, for instance.

During downturns, there is also a “flight to quality.” This is good news for those of us focused on high-end quality in our products and services. This is true for Core Facilities like you as well as tool providers like us. Only those of us who bring unique value survive during times like these, and we alone will thrive once recovery gets under way.

Indeed, the future outlook is brighter than ever for those who have special expertise in the right domain. In fact, I believe there are special opportunities ahead for those well-versed in advanced proteomic data analysis.

The “Digital Biology” revolution happening now will change everything
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If you have attended a conference lately, such as the ASMS in Denver, you would have found a bewildering array of exciting new products and ideas for your advanced proteomic mass spectrometry research. 

More than ever, there is a need to remain focused with both your resources and efforts. Now is a good time to use the “80-20 Rule” to cut through the clutter and sharpen your focus. 

The 80-20 Rule (also called the “Pareto Principle” or the “law of the vital few”) states that in many situations 80% of the effects come from only 20% of the causes. It readily applies to many aspects of mass spectrometry and proteomic research.

Focus on the Vital Few in Proteomics

The key to success is to remain focused on what is truly significant, by strategically investing your resources on the “vital few” products, technologies and people with the highest impact to you. 

Here are some of the ways that the 80-20 Rule may apply to your proteomic research, and how you can sharpen your focus.

Invest in Quality

Less than 20% of today’s products account for 80% of overall sales. The rest (80%!) will fade away. Invest only in high-quality products that thrive, while avoiding products that will disappear.

Ideally, you want to get word-of-mouth references from trusted colleagues before purchasing critical tools for your focus areas. This is especially true for software products, some of which are laden with incomplete features designed to be demo’ed and sold rather than used.

With today’s limited budgets, it is important to invest in solid tools rather than to buy the latest widgets. Avoid the temptation to buy inexpensive rather than high-quality, well-supported products. (Most people find that the costliest products are the cheap ones they buy but do not use.)

To optimize your tools purchase, start with a prioritized “Top 10″ capabilities list, then focus on a workflow that can solidly deliver the top 2 must-haves as well as some number of the remaining 8. Given today’s tool market, you will need to integrate tools from different sources to address most of your key requirements.

For the top 2 must-haves, the question is never a yes/no question of whether a certain capability (e.g. ETD) is supported, but how well. Do not choose tools on the basis of the length of the features list. And you may find that technical support can be at least as important as the product itself in a highly technical, evolving field like proteomics. 

Pamper your Workhorse

Perhaps 20% (i.e. 1 of 5) of your mass spectrometers may impact 80% of your research by generating 80% of the spectral data. For example, many labs with several different mass spectrometers tend to have one workhorse instrument, commonly a fast-scan ion trap (e.g. Orbitrap or LTQ) or Tof/Tof (e.g. 4700) mass spectrometer.

If that is the case in your lab, allocate your resources according to impact, and focus at least half your analysis budget on the one key instrument. Avoid the mistake of having the majority of the mass specs dictate the workflow of your most important one.

With tools like PeptideProphet and Scaffold that can accommodate different search engines, you can tailor the search engine to each mass spec, while maintaining a consistent high-level workflow optimized for different instruments.

Associate with Leaders

Perhaps 20% of the researchers seem to publish 80% of the papers and get 80% of the funding. You need to be part of this elite class. How? By doing top-notch work and focusing on your unique value-added capability to the existing network, while minimizing distractions from low-value activities (particularly IT issues).

Whether in elite athletics like the Olympics or science, winners associate with winners. To be part of the winner’s circle, you need to maintain the winner’s mindset, use the professional quality tools and methodologies, and bring yourself to that top level in terms of knowledge, expertise, and professionalism.

The best way to get started is to first replicate the workflow used by leaders in the field, which is more efficient than starting from scratch. The workflow will serve as a good foundation for adding your own unique capability while leveraging an existing high-performance infrastructure.

An Integrated Workflow System for World-Class Proteomics

For more than six years, Sage-N Research has worked with the world’s top technologists to develop a professional quality, server-class integrated proteomics analysis platform targeted for the top 20% proteomics laboratories expected to make the greatest impact.

The result is the Sorcerer 2 system, which delivers a robust workflow incorporating the best technologies from the laboratories of our Scientific Advisory Board members — Drs. John Yates, Steven Gygi and Ruedi Aebersold. In the near future, the Sorcerer 2 platform will incorporate ETD/ECD analysis technologies from Dr. Roman Zubarev, our newest scientific advisor. 

The Sorcerer 2 system is designed to fill in an important gap for advanced “Proteomics 2.0″ analysis, by delivering a standardized workflow platform that can accommodate 80% of standard proteomics analyses right out of the box, while providing an integrated “MUSE” scripting environment to allow user-customizable post-search analyses and workflows for the remaining 20%. This allows labs to focus on scripting their own unique analysis IP while leveraging an existing powerful workflow system.

Biotechnology is widely considered the Next Big Thing due to the rapid rate of scientific advances made possible by new technologies and their expected socioeconomic impact. With the advent of proteomic mass spectrometry, there are now post-genomic technologies for characterizing all three polymeric biomolecules: DNA, RNA, and proteins.

Of the three technologies, automated protein characterization (i.e. proteomics) holds the greatest potential for revolutionizing biology and drug discovery. Why? While RNA is used to infer the biochemical pathways, proteins are the biochemical pathways.

With the current generation of “Proteomics 2.0″ technologies focusing on protein modifications, this may be the Tipping Point* for the revolution in industrial biopharmaceutical research, especially as current proteomics evolves from being merely usable to increasingly sensitive and powerful.

Here’s what to expect in the next few years, and how you can position yourself to contribute to and benefit from the impending Biotech Industrial Revolution.

Proteomics 2.0 brings Relevance

First generation proteomics focused on generating lists of identified proteins, which by itself was of marginal interest to drug companies. As a result, it was used mostly by academia for academic-quality research and publication. 

Most first generation software tools and associated ad hoc workflows were designed more for rapid publication than for sensitive, robust results required by industrial research. Indeed, industrial-quality software tools were often shunned in favor of cheaper, feature-rich (but less robust and less sensitive) software. 

In the last two years, proteomics has evolved to focus on relevance, as proteomic scientists become more excited about results than capability (e.g. profiling phosphorylation sites rather than getting 2 ppm mass accuracy).

This next generation “Proteomics 2.0″, which focuses on post-translational modifications (PTMs), particularly phosphorylation and ubiquitination, is now increasingly relevant to pharmaceutical and biotechnology companies already interested in kinase inhibitors, oncology, stem cells, and neurodegenerative diseases. For high-precision phosphorylation profiling at a meaningful scale, there is currently no alternative to proteomic mass spectrometry.

Industrial-quality research, done by either academia or industry, requires sensitive tools, industrial-quality workflows (i.e. duc tape and prayer not allowed), and robust results that are reproducible and can stand up to validation. After all, ambiguous or misleading results can cost drug companies millions of dollars during validation and impact a billion dollars in lost sales and product delays. 

As the value of the proteomic workflow shifts from capability to outcome, the backend data analysis and the analytical ability of the scientist become more important than the instrumentation. This is especially true when the instrumentation becomes standardized and commoditized, while the experiments of interest require increasingly more sensitivity and sophistication.

Mindset to Success

More than any post-genomic technology, proteomic mass spectrometry offers the best opportunity to begin to trigger the Biotech Industrial Revolution. This is good news if you are active in proteomics, whether you plan to remain in academia working with industry or you plan to work in industry. (In any case, industry is where you will find the funding necessary to drive the really big breakthroughs with economic value.)

Many important technology-based fields like semiconductors, software, and the Internet had their greatest window of opportunity during economically challenging times. Biotechnology is probably no different. 

In any field where the outcome is very important, professionalism is the key to success. This means having a professional attitude, using professional-quality tools, and being an expert in all key aspects of your specialty. 

Photography professionals focus on getting the perfect shots, use heavy-duty professional cameras and tripods, and understand the intricacies of exposure time, lighting conditions, and film speed. Others just take pictures here and there, use simple point-and-shoot cameras, and may have no idea what an f-stop is. 

Under favorable lighting conditions, an amateur may even “validate” his point-and-shoot camera as taking better pictures, especially if he is comparing it against a more complex professional camera for the first time. Regardless, when national sports magazines need the best pictures, they go to the pros.

In proteomics, professional practitioners may be akin to tax attorneys, in that we work with hard numerical data and yet will come up with different results based on our level of expertise. If you plan to be a professional proteomics practitioner, make sure you get professional-quality tools designed for robust, sensitive results. If you are using the easiest rather than technically the best tools, and you have little idea how the results from your search engine and other software are computed, a professional upgrade may be in order.

If you have questions about specific recommendations for your own situation, please contact us.

*Note: The Tipping Point is a best-selling book by Malcolm Gladwell (2000) who observes that huge changes are often caused by small things that happen at the just the right time under just the right conditions.

Many research labs are experiencing funding reductions. Keep in mind that recessions, like boom times, will come to pass. The key is that, because proteins will likely not go out of style in medical research, automated protein characterization — that is, proteomics — will have an increasingly important role. I would go so far as to make a prediction that a Nobel Prize discovery in cell signaling will be started with a proteomics experiment in the next 3 years, based on the recent readiness of large-scale proteomics technology and the rapid progress in the science of cancer and stem cells. (Remember - you read it here first!)

However, changing times require a changing strategy. When funding is tight, it is important to focus on preparing yourself for the recovery. A recession has the effect of thinning the field by eliminating the weaker players. The silver lining is that it also enhances the relative position of the stronger players, as well as makes the whole field more efficient. In fact, those at the top of their game are given a rare opportunity to pull far ahead of their peers to firmly establish their reputation.

The trick is to prepare yourself to become more relevant scientifically, so you will survive the recession and thrive once the recovery starts. Here are some specific suggestions for you, the proteomics scientist, to make yourself and your lab more valuable while the times are lean.

Differentiate yourself with specialized expertise

More than ever, it is important to be differentiated from your peers. At one time, owning a high accuracy instrument was enough, but not now. With many labs possessing nearly identical setups, it is important to differentiate yourself by being able to perform more complex experiments and getting higher quality results. 

If you run a proteomics facility, this is the time to become competent in larger MudPITs, phosphorylation profiling, and quantitation. Think about it this way. If you establish your lab as the being the best at phosphorylation analysis within a 100 mile radius, you will likely be as immune as possible from budget cuts. On the other hand, if you are still using your $600K mass spec for nothing more than simple gel spots, then the recession will put your role at risk.

With approximately 30% of the drug development programs based on kinase inhibitors, phosphorylation analysis is probably the hottest area within proteomics right now. With tools such as Harvard’s Ascore algorithm, large-scale phosphorylation site localization is within reach of many labs.

Invest in tools, automation, and education

This quiet period is a good time to invest in yourself in terms of learning new software and tools, increasing your level of automation and efficiency, and generally deepening your core competency. Remember, the objective to be best prepared to ramp up quickly once the recovery starts.

If you didn’t have the time to fully understand all your analysis tools before, this is a good time to backfill the knowledge. Learn about new search engines (e.g. Phenyx, X!Tandem), productivity tools (e.g. Scaffold, Trans-Proteomic Pipeline), and specialty software (e.g. Ascore). The good news is you can learn and try all of these tools for free! Also, Ionsource.com provides some well-written tutorial material suitable for new proteomics practitioners. 

If you run a proteomics facility, make sure you have quality tools, and that you have a high level of understanding on how they work. It’s not longer enough to rely on “magic software” to supply all the answers, because none of the software today is sophisticated enough to tell right from wrong without expert judgment for all but the most simple experiments.

Focus on your core competency

During recent years, many proteomics labs branched outside their biochemistry and mass spectrometry expertise into cluster computer administration, search engine development, and custom software development. While some of these efforts result in pushing the technology envelope, others are best characterized as a distraction and dilution of focus.

During leaner times, it is imperative that you refocus on your core competencies, as this is the most dangerous time to lose focus.

Instead, this is the best time to establish collaborators, partners, and vendors whose core competencies complement yours. Doing so will enhance your productivity, increase your leverage, and improve your focus. That is the best preparation when the recovery begins.

Is your Mass Spectrometer the key to drive Cell Biology Discoveries?

Mass spectrometry-based proteomics has been described as the “protein microscope” instrumental in several key advances in cell biology, including protein composition of cellular organelles and protein interaction networks (Bell et al, 2007). The protein microscope will become even more powerful with the recent software tools for statistically robust analysis of million-plus spectra experiments.

If your mass spec lab already has the sample prep expertise and modern instrumentation (for example, Acuity HPLCs and Thermo LTQ mass specs are well-respected instruments), a quality high-throughput software workflow may be all that is missing from your protein microscope that will drive the next major discovery.

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Times are changing fast

In 2003, a Nature Biotechnology article title declared, “Data analysis - the Achilles heel of proteomics.”

In 2008, this is still true for most researchers, but it need not be any longer. Today’s analysis workflows are more powerful, accurate, and better integrated than that of 5 or even 2 years ago.

It’s the software that will make the difference

If you’re working in an important field like stem cell or cancer pathways, then you may be just a few key proteins away from a fundamental and groundbreaking discovery. If you have a sensitive mass spec like an LTQ-Orbitrap® or an LTQ®, you already have the basic “hardware” to make those earth-shattering discoveries.

But if you are like most mass spec researchers today, you may lack the right “software,” including both the tools and the know-how, to sensitively and accurately characterize those subtle proteins in your samples.

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