2012-2-09

Register for ASMS 2012 - PEAKS User Meeting

Waterloo, Ontario - Registration is now officially open for the ASMS 2012 User Meeting in Vancouver, Canada. The user meeting will be held in the Pacific Rim Suite 2 in the Pan Pacific Vancouver Hotel. For full event details and to register for the meeting click here.

2012-1-10

MCP: PEAKS DB Publication

Waterloo, Ontario – "PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification." Database searching is the most common form of protein and peptide identification and researchers prefer this approach as it is very fast and very familiar. But is it the best? The danger is when the decision for speed takes priority over accuracy. While a 0% FDR is highly unlikely for any automated process without removing some quality candidates, there is one method which ensures the lowest FDR while maintaining high sensitivity. The approach integrates de novo sequencing results into the database search.

“PEAKS DB achieves significantly improved accuracy and sensitivity over two other commonly used software packages. Additionally, a new result validation method, decoy fusion, has been introduced to solve the issue of over-confidence that exists in the conventional target-decoy method for certain types of peptide identification software.”

The full publication can be obtained from the MCP website.

2011-12-01

PEAKS Challenge Winner Announced

Waterloo, Ontario - BSI has officially concluded the PEAKS 5.3 Challenge and selected a winner, Arttu Heinonen from the University of Turku. We would like to thank everyone who participated in the PEAKS Challenge. We are extremely pleased to see how well PEAKS performed against other available database search engines. Arttu Heinonen was randomly selected from the list of participants who submitted a screenshot of the inChorus Summary Pane showing a comparison of PEAKS DB and third-party search engines (such as Mascot, Sequest, X!Tandem, OMSSA).

Since we are enthusiastic about algorithms, drawing a name from a hat would not suffice...

To randomly select the winner from the submissions we performed the following steps:

• Numbered the participants from 1...n (n = number of submissions)
• Selected the Dow Jones Industrial Average Closing Value from November 30, 2011 (12045.68)
• Round to the closest integer (12046)
• Divide by number of participants (n)
• Use the remainder as the winner (0.875*n = winning participant’s number)

1. The ability to generate high-confidence de novo sequence tags
2. DB Result Summary View, providing all the necessary statistical charts for result validation and publication
3. inChorus results, showing multiple search engines' peptide identification results side by side.

2011-08-15

PEAKS Online 5.3 Released - Accurate and Sensitive Peptide Identification

Waterloo, Ontario - Bioinformatics Solutions Inc (BSI) today announced the release of PEAKS Online 5.3, the server edition of the popular PEAKS Studio software for proteomic mass spectrometry research. Finally, increased coverage, confidence and low false discovery rates are available to the server accessible market.

Since the release of PEAKS Studio 5.3, users have been realizing that PEAKS is more than just a standard database search tool...even more than just a de novo sequencing tool. Most users with a basic understanding of the software are noticing the significantly improved coverage provided, when compared to their other search engines. Comparisons have been made via manually sifting through the data as well as automatically through the inChorus features provided in PEAKS.

The new software is for more than just existing customers with server solutions. The new PEAKS Client (server access tool) is also available as a free download to non-users, offering access to an optional public server hosted by BSI.

As noted during the Studio release, greater confidence is achieved by utilizing PEAKS DB's built-in result validation, offering quality assurance at a glance. Whether studying an unsequenced organism, sequencing synthetic peptides or analyzing known proteomes, PEAKS is the right tool for you.

"The PEAKS solution offers a best-in-class accuracy and sensitivity that researchers love. We know researchers will be impressed by the faster performance and easy to understand summary pane delivered by this new tool." - Brian Munro, BSI.

2011-06-16

PEAKS 5.3 Released (Accuracy & Sensitivity)

Waterloo, Ontario – Bioinformatics Solutions Inc, makers of PEAKS software, released the latest version of PEAKS Studio 5.3. The significantly increased accuracy and sensitivity of PEAKS DB (database search engine) performed excellently in the ABRF PRG 2011 study, as well on early evaluator’s data.

“A big step forward.”

“Far better than I could ever squeeze out of my data."

In addition to PEAKS being the preferred de novo sequencing software, the latest version (5.3) provides a superior database search engine offering greater coverage, confidence and low false discovery rates. Greater confidence is achieved utilizing PEAKS DB’s built-in result validation, offering quality assurance at a glance.

The unique new “de novo only” view of PEAKS DB displays many potentially novel peptides found in your sample, otherwise missed by exclusively database searching.

Whether studying an unsequenced organism, sequencing synthetic peptides or analyzing known proteomes, PEAKS is the right tool for you.

The release was announced during the BSI team’s annual meeting at ASMS, this year in Denver, Colorado at the Sheraton Hotel – Downtown. For those unable to attend, further details including research presented and software details are available on the meeting’s page.

2011-04-19

PEAKS at ASMS 2011

Waterloo, Ontario – Bioinformatics Solutions Inc, makers of PEAKS software, will be hosting a Sunday meeting at ASMS 2011 in Denver, Colorado at the Sheraton Hotel - Downtown. All users are welcome to attend, although registration is required and space is limited.

Visit our ASMS page to view time, location and other information now. Also, after the show posters and additional resources will be posted on this link, so be sure to bookmark it for when you return.

2011-02-14

PEAKS performed excellently in ABRF/iPRG study for ETD MS peptide identification

Waterloo, Ontario – The iPRG group of ABRF 2011 conference hosted an independent study for researchers to benchmark their own labs' ETD data analysis capability. Thirty-five labs worldwide submitted their peptide identification results using the same dataset provided by iPRG. Researchers using PEAKS software performed excellently and identified a considerably high quantity of peptides with a very low false discovery rate (FDR). This is just another study illustrating the exceptional capability of PEAKS software in providing a combination of high peptide identification rate and low FDR from database searching. According to Dr. Bin Ma (CTO, Bioinformatics Solutions Inc.), this is made possible by combining the reputable PEAKS de novo sequencing results in the database search analysis.

Visit this link to view the original slides presented by the iPRG: here.

2011-02-10

De Novo Sequencing Webinar Sessions

Waterloo, Ontario – In addition to the regularly scheduled webinars, providing an overview of PEAKS’ features, BSI will introducing a second webinar series, dedicated to de novo sequencing. The meeting will break things down into three areas: How de novo sequencing works, what makes PEAKS different and how to apply in the software. To sign up for the next available session, email your sales representative or email This e-mail address is being protected from spambots. You need JavaScript enabled to view it . Dates and times are available on the PEAKS webinar website.

2011-02-05

Research: GlycoMaster - Software for Glycopeptide Identification with Combined ETD and CID/HCD Spectra

Waterloo, Ontario – To automate the data analysis process for the identification of glycopeptides with combined ETD and CID/HCD fragmentation. Click link to view poster for GlycoMaster.

2011-01-30

PEAKS Free Webinar Training

Waterloo, Ontario – BSI offers regularly scheduled online training sessions for users to learn how to most efficiently and effectively use the PEAKS software. We break down the software in to each of its components, explain what they do, then put it all back together in an easy to navigate workflow, as well as explain the results. This gives users an opportunity to learn about features, perhaps having gone unknown, as well as ask questions. In addition to these group training sessions, feel free to contact your sales representative if you would like to have a personally guided one-on-one training session. Dates and times are available on the PEAKS webinar website.

2011-01-25

Research: PEAKS DB - Substantially Improved Peptide Identification

Waterloo, Ontario – Peptide identification is a central task in mass spectrometry based proteomics. Existing approaches include: (1) protein sequence database search with uninterpreted spectra, (2) de novo sequencing, (3) database search of de novo sequence tags, and (4) spectral library search. These approaches are usually performed separately according to the circumstances. In this abstract, we present the PEAKS-DB software that combines the first three approaches to significantly improve the sensitivity and reduce the FDR of peptide identification.

Click link to view poster for Substantially Improved Peptide Identification.

2010-11-08

Server Software Release: PEAKS Online 5.2

Waterloo, Ontario – Bioinformatics Solutions Inc (BSI) has released the latest version of the much anticipated proteomic mass spectrometry server software, PEAKS Online. After many years in development, the server/cluster solution of PEAKS provides almost an identical resource for in depth investigation as the desktop solution (PEAKS Studio) with all the advantages a high throughput processing server has to offer.

For many years, PEAKS Online offered a web based interface for users to send and receive data between their desktop and server. PEAKS Client continues to provide a direct connection to the server (PEAKS Online) with support for direct import of instrument files as well as highly detailed results views; although this time all processing is performed by the server.

Additional features to PEAKS Online's famous de novo sequencing and protein identification search engine include inChorus, SPIDER and PTM Finder. inChorus is a multi-engine protein ID tool, enabling existing results from PEAKS, Mascot, OMSSA, and X!Tandem to be combined into a single consensus report. The advantage to users is high confidence results through agreement between engines and the removal of false positives. The SPIDER homology search tool utilizes confident de novo sequence tags to search for homologous proteins in a database. Reconstruction of the sequence can account for mutations and/or sequencing errors and increase protein coverage by up to 18%. Furthermore, using PTM Finder can increase identification scores by considering user-defined modifications while optimizing processing time, as this is a post-database search utility.

Users are encouraged to take advantage of the shared resource, Public PEAKS Online available at www.bioinfor.com/peaksonline and download the necessary applications for processing jobs remotely on the BSI server.

For a guided tour of the software, please contact our sales team or join one of our regularly scheduled public webinars. Additionally, PEAKS Studio is available on a 30 day free trial basis. Customers also have the ability to join the public webinars or request personally guided (private) sessions to improve their understanding of the tools found in PEAKS. PEAKS provides many unique and innovative tools with an emphasis on high confidence and accuracy. PEAKS, welcome to the top!

2010-06-10

PEAKS Studio 5.2 Release

Bioinformatics Solutions Inc. (BSI) has released the latest installment of PEAKS Studio (version 5.2), a proteomic mass spectrometry software specializing in identification (de novo sequencing, database searching, homology searching, multi-engine protein ID) and quantification (labelling and label free). With the addition of increased de novo and database search accuracy and speed, this version offers result comparison, automated precursor mass and charge correction for high resolution data & numerous applications for journal publishing, such as MCP result exporting. Not to be outdone, PEAKS Q (an optional quantification node) now supports replicate analysis (for label free), greater options for normalization and overall improved results.

2010-03-18

Dr. Bin Ma, 2010 Outstanding Young Computer Science Researcher

Chief Technology Officer of Bioinformatics Solutions Inc. and Professor at the University of Waterloo, Dr. Bin Ma, was recently recognized by the Canadian Association for Computer Science (CACS) as an Outstanding Young Computer Science Researcher.
“CACS’ research prizes recognize young computer science faculty members at Canadian universities within 10 years of their Ph.D. who have made highly significant research contributions to the field of computer science,” Tamer Özsu, Director of the David R. Cheriton School of Computer Science at the University of Waterloo.
Further details will be provided on the Canadian Association for Computer Science website.

2010-04-14

Dr. Ming Li, 2010 Killam Prize Recipient for Engineering

Dr. Ming Li is currently being recognized with the 2010 Killam Prize in Engineering. The Killiam Prize annually recognizes leading Canadian scholars in five distinct areas of research: humanities, social sciences, natural sciences, health sciences and engineering, presented by The Canada Council for the Arts.
"Dr. Ming Li is one of a handful of internationally acclaimed computer scientists whose research has had major impacts outside his own discipline. His work is now finding new applications in computer science, bioinformatics, philosophy, physics, and statistics… Dr. Li's innovative work in the fields of computer science and bioinformatics has already moved well beyond theoretical investigation into exciting new ways to examine the sequence, structure and function of living cells."
Further details are provided on the Canada Council website.

2010-02-08

RAPTOR 4.5 Software Release (Protein Modeling)

Waterloo, ON, Canada- Bioinformatics Solutions Inc. announces the launch of protein modeling software, RAPTOR 4.5. This is the latest edition of the renowned protein threading algorithm, introducing a convenient project management system for stable operation of multiple sequences.

Academic and corporate professionals are noticing the advanced GUI providing a greater level of detail, particularly about alignments, which in turn provides more complete information about the sample as a whole. Right from the get-go, the improved reporting and graphics are making more users feel at ease with the research tool. In addition to the graphical enhancements, organization was a feature many users were requesting. "Project management was a clear direction we have wanted to take the software for some time, but there were other important features that always seem to have a commanding focus. Users are now going to have an easier time keeping track of high sample throughput." Zia Rahman, RAPTOR engineer. The RAPTOR software is readily available to users for free trial licenses, complete with technical support. Further information can be found on the RAPTOR website: www.bioinfor.com/raptor

2009-09-24

ZOOM 1.3 GUI Release (Next Gen Seq)

Waterloo, ON, Canada- Bioinformatics Solutions Inc. announces the launch of next generation sequencing software, ZOOM Studio 1.3, in a user-friendly GUI, integrating the short sequence mapping, result display and post-analysis tasks.

For the mapping task, the new architecture of ZOOM can automatically schedule large volumes of data on a standard PC or across multiple computers with multiple cores. As before, ZOOM supports nucleotide reads from Illumina/Solexa instruments and color space reads from ABI SOLiD instruments, allowing both mismatches and insertion/deletions for single-end and paired-end data sets with read length from 15bp to over 200bp. ZOOM now introduces a unique framework to construct efficient spaced seed sets capable of achieving 100% sensitivity for a large range of read lengths and mismatch numbers.

Mapping results are presented clearly, complete with tools for zooming in and out (from the read depth overview along the reference sequence to read alignment details). Read depth peaks are useful for easily locating interesting mapping clusters.

For post-analysis, ZOOM assembles mapping results into a haploid or diploid consensus sequence. Potential SNP and short INDEL sites are reported, ready for navigation along reference sequences, adopting various user specified filtering criteria. Further, mapping results can be exported in BED and GFF formats, as well as the WIG format to aid in further study with the UCSC genome browser.

2009-08-26

Living a Dream, Dr. Bin Ma, Bioinformatics Solutions Inc.

Biologists and pharmaceutical researchers often need to know what proteins are present in biological samples. Mass spectrometry has become the standard way to procure this information. Through the use of computer software and manual research, researchers are able to analyze this data and report what proteins are in the sample. However, one problem that bioinformatics researchers have had difficulty with is finding a precise way to identify novel proteins.

It took Dr. Bin Ma to succeed in finding a solution to this problem. As the chief technology officer with Waterloo-based Bioinformatics Solutions Inc., Dr. Ma has helped develop multiple products that are now used by leading pharmaceutical companies, biotechnology firms, research hospitals, government labs and university research centres for the purpose of protein identification. These products, PEAKS and PatternHunter are able to not only report what proteins are in a sample but also identify novel proteins.

Full Article

2009-08-25

PEAKS Viewer 5.1 Release

Proteomic research is as much about discovery as educating others of these findings. That is why BSI, makers of PEAKS Studio, released a brand new PEAKS Viewer software, offering researchers greater abilities to share results with colleagues and collaborators at no cost. This application is designed to provide users with the ability to view results of processed data within PEAKS projects.

PEAKS projects provide stability, organization, not to mention highly accurate findings from all research tools found within PEAKS Studio (de novo results, database PEAKS Protein ID results, PTM Finder results, SPIDER results and Quantification results, etc).

Visit the PEAKS Viewer page to read more and share your findings.

2009-08-10

RAPTOR 4.4 Release

Waterloo, ON, Canada- Scientific software specialists, Bioinformatics Solutions Inc. (BSI) announced the release of their latest protein structure modeling software, RAPTOR 4.4.

RAPTOR 4.4, recognized annually in CASP competitions as a leading method for reliable protein structure modeling, expanded its core application to provide users with greater functionality. Among features introduced with this version, users can now update internal PDB template libraries and read PIR alignment files to process with OWL. OWL is a subsidiary application to RAPTOR, that ensures optimal structure accuracy and completion. Further, users can select alignments from either threading output or BLAST output and specify further alignments to model the 3D structure, using OWL.

2009-07-28

Made-in-Canada Software Probes Building Blocks of Life

Bin Ma started Bioinformatics Solutions in 2000 and the company is already widely recognized for its award-winning PEAKS Software. The product is able to assist chemists in identifying completely new proteins that could be used in developing new drugs or detecting diseases even before birth. It is faster and more accurate than anything else on the market, according to one chemist.

Most lay people reading the results of a mass spectrometry peptide analysis, wouldn't make head nor tails of it, but with Randy Whittal it's a different story. Used to poring over such data for hours and manually putting together the puzzle pieces that when completed, for Whittal the analysis would reveal a brand new biological structure.

Peptides, or small proteins, are a collection of amino acids, strung together to create life. Without these basic strings of biological matter that emerged from the Earth's primordial soup, humanity - and all life on Earth - simply wouldn't exist. It's no wonder that modern-day chemists are looking for the best tools available to help them understand these building blocks of life.

For Whittal, the director of mass spectrometry in the department of chemistry at the University of Alberta, a pencil and paper powered by his own brain was the best tool to do that. Until he found PEAKS software, powered by Waterloo, Ont.-based Bioinformatics Solutions Inc.

Full Article

2009-07-13

PEAKS Studio 5.1 Release (Protein ID & Label Free Stability)

Waterloo, ON, Canada- Bioinformatics Solutions Inc., globally renowned for scientific software, announced the release of its latest and most advanced software solution, PEAKS Studio 5.1, for MS/MS proteomics.

The tandem mass spectrometry software provides necessary tools for various proteomic investigations, such as de novo sequencing, protein identification, quantification (label and label free methods), batch workflows and stability for files of all sizes, few megabytes through hundreds of gigabytes.

Proteomic researchers using MS/MS are generating much larger file sizes attributed to advancements in instruments. Welcoming the rich content extracted by the newest instruments, PEAKS took an early initiative to support extremely large file sizes. While successful with extremely large files, PEAKS Studio 5.1 provides advancements for more commonly sized RAW files, with increased stability.

While PEAKS de novo sequencing remains an industry standard, advancement to quantification methods, specifically the label free, are provided with PEAKS Studio 5.1. To hedge improper parameter settings, leading to ratio deviation, PEAKS provides users with straightforward visual inspection tools for analysis of raw spectra, to confirm accurate analysis. PEAKS allows researchers the flexibility to adjust parameter settings in order to gain greater accurate ratios with the aid of a 2D view of the MS/MS spectrum as well as a 3D view of the parent scan for each identified peptide. Thus actual ratios can be easily verified against corresponding raw spectra.

2009-05-13

BSI Co-Founders Win Two Premier Awards for Innovation

Co-Founders of Bioinformatics Solutions Inc. and professors at the University of Waterloo, Dr. Ming Li and Dr. Bin Ma each won respective awards last night at the 2009 Premier Awards in Toronto, Ontario, Canada. Dr. Li was presented Premier's Discovery Award for Innovation Leadership while Dr. Ma won the Premier's Catalyst Award for Best Young Innovator.

The Ministry of Research and Innovation, a branch of the Government of Ontario, selected Dr. Li and Dr. Ma independently, based on their research applications to the field of bioinformatics and algorithm design in mass spectrometry respectively.

"The Ministry established this world-class innovation awards program to recognize our most creative and successful entrepreneurs." Craig Fowler, Director (A) Research Branch, Ministry of Research and Innovation.

Dr. Li's Premier's Discovery Award for Innovation Leadership is highly attributed to his successful efforts with numerous bioinformatics software, PatternHunter (general purpose homology searching), RAPTOR (protein modeling) and PEAKS (protein identification), as well as his founding of the University of Waterloo's co-operative undergraduate bioinformatics program, rated among the elite in North America.

The Premier's Catalyst Award for Best Young Innovator recognizes Dr. Ma's research towards the proteomic mass spectrometry software, PEAKS. First released in 2002, PEAKS has gained widespread acceptance by pharmaceutical companies, governments and academic institutions worldwide, for its reputable identification of protein sequences with and without the aid of a database. The most recent developments for PEAKS are dedicated to sample quantification (labeled and label free) as well as the continued efforts in sequence reconstruction.

These awards not only recognize the great minds behind cutting edge innovations, such as Dr. Li and Dr. Ma, but further contribute to a rapidly growing interest in BSI's ongoing research initiatives and bioinformatics development as a whole.

2009-02-04

PEAKS Studio 5 release - Get more from your mass spec data

(Waterloo, ON, Canada) Bioinformatics Solutions Inc released their latest proteomic tandem mass spectrometry software solution, PEAKS Studio 5, earlier today. Recognized globally for de novo sequencing (identifying peptides not found in databases) and meta protein id tool, inChorus, PEAKS Studio welcomes this latest edition to its growing product line.

Loading and processing enormous RAW files, such as in excess of 35 Gigabytes, represents BSI's commitment to supporting instrumentation technological innovations. How many other ms/ms software can perform this task...on a laptop! No longer a secret this solution derives from the introduced project based management approach. This approach allows users to easily process multiple runs, and simultaneously compare, combine, filter the results together for straightforward interpretation.

For cases where neither a database nor protein identification yields a viable solution, there is an improved SPIDER tool, for sequence reconstruction. Not only are more accurate results produced, but in a fraction of the time... 14 times faster than before... and people thought it was fast before. SPIDER also now supports both fixed and variable PTMs. Quantitation is also introduced with this release. Provided seamlessly within PEAKS Studio 5, this available node supports ICAT, iTRAQ, SILAC, and all other label methodologies. Be sure to check out the new look of PEAKS Studio 5 at www.bioinfor.com today.

2008-11-06

RAPTOR 4.2: Protein Structure Prediction Release & CASP8 Results.

Waterloo, Canada -- Bioinformatics Solutions Inc. is proud to announce the release of RAPTOR 4.2, a protein threading software package, ranked as one of the very top servers in CASP8 (Critical Assessment of Techniques for Protein Structure Prediction 2008) for all targets, for the fourth consecutive competition.

RAPTOR accurately predicts protein structures by threading a query protein sequence through structure template libraries. The latest edition of RAPTOR, version 4.2, offers a new internal 3D structure modeling application to eliminate the need for expensive third-party Modelling software. Further RAPTOR applications include three different threading engines and a homology search module (PSI-BLAST based).

CASP is a community-wide competition to advance the field of protein structure prediction taking place every two years since 1994. Ranking for this competition is based on more than 80 protein structure prediction servers worldwide. Protein structures that are either expected to be solved shortly or that have been recently solved, yet to be released to the public are used as targets for the prediction. Each server's performance is measured by the sum of its prediction quality scores for all targets. Several assessment groups perform independent rankings. According to the ranking list generated by TM-score, RAPTOR is placed 2nd among all the servers. The well-known ROBETTA server is ranked number 5 in the same list.

RAPTOR first appeared in CAFASP3 (CASP5) in 2002 and was ranked number one in the individual server group for that year. Since then, RAPTOR has actively participated in every CASP and received consistently top rankings. The RAPTOR software package is provided by Bioinformatics Solutions Inc.

2008-09-12

CASP Ranks RAPTOR 2nd

Bioinformatics Solutions Inc. is proud to announce that RAPTOR, our protein structure prediction software, placed 2nd in this year's CASP competition (CASP8). With more than 80 protein structure prediction servers and more than 100 human expert groups, the biennial CASP competition is the Olympic games of the protein structure prediction field. The object of this worldwide competition is to predict the 3D structure of a protein from a description of its contents at a molecular level. RAPTOR has participated in the CASP competition since 2002 and has consistently ranked in the top tier, indicating our commitment to a quality product. The RAPTOR software package is commercially available from Bioinformatics Solutions Inc (Waterloo, Ontario, Canada). RAPTOR is a user-friendly program that uses three different threading engines as well as a homology modeling module derive protein structure.

2008-03-31

Identifying Unique Folds using RAPTOR for Protein Structure

Hui Li et al. recently investigated the transcriptional activity of C/EBP-A, and have published their findings in the Journal of Biological Chemistry, after identifying unique folds using RAPTOR for protein structure prediction. As the authors state, "transcription factor C/EBP is crucial for regulating transcription of genes involved in a number of diverse cellular processes, including those involved in some cytokine-induced responses. However, the mechanisms that contribute to its diverse transcriptional activity are not yet fully understood." The use of transcriptional mediator regulates signal-induced cellular gene transcription from enhancer-bound transcription factors in the multi-subunit protein complex. As is the rising case with many researchers, the preferred method for determining the protein structure was completed successfully using RAPTOR.

The preference comes from its strength in hard targets, cases with low or no sequence homology. Typically, given a target protein sequence, comparison with a homologous protein with known structure can be found by using sequence search tools like PSI-BLAST or BLASTP. The target's structure is then built from the known structure. However, when sequence homology is not significant, i.e. less than 25%, PSI-BLAST and BLASTP can not provide confident result. Unlike PSI-BLAST or BLASTP, which simply does a sequence search, protein threading (fold recognition) makes use of both homology and structure information. It scans the protein sequence with an unknown structure against a database of known structures. By using a scoring function and conducting compatibility analysis between three-dimensional structures and linear protein sequences, the best structural template will be identified from which to build the sequence's structure. As a result, protein threading gives a superior prediction than homology modeling when there is no sequence homology. In this particular case domain confirmation was modeled in addition to accurately identifying the critical region of cellular factor of C/EBP. BSI would like to congratulate each researcher of this project on their investigation and findings. Contributing authors include: Hui Li, Padmaja Gade, Shreeram C. Nallar, Abhijit Raha, Sanjit K. Roy, Sreenivasu Karra, Janardan K. Reddy, Sekhar P. Reddy and Dhananjaya V. Kalvakolanu.

2007-12-17

2 Best Paper Awards

Bioinformatics Solutions Inc (BSI) would like to applaud two "best paper awards" by BSI authors Ming Li and M. Ziaur Rahman, in prestigious international conferences this year (2007). "FragQA: predicting local fragment quality of a sequence-structure alignment," by Li and his students at University of Waterloo, claim the Best Paper Award at the Genome Informatics Workshop (GIW) in Singapore. The report is expected to add an important component to RAPTOR, for predicting protein structures. GIW is the longest running international bioinformatics conference, devoted to the computational understanding of biological systems on a molecular basis. M. Ziaur Rahman and University of Waterloo SCS Professor J. Ian Munro won the "Best Paper Award" for their report "Integer Representation and Counting in the Bit Probe Model" presented at the 18th International Symposium on Algorithms and Computation (ISAAC) 2007 in Sendai, Japan. The research paper addresses the methodology of representing integers so that updates to values can be performed in a power efficient manner. ISAAC is currently hailed as the leading field of Algorithms conference in the Asia-Pacific region. Rahman has recently accepted a position at BSI as a software developer and research analyst for RAPTOR.

2007-10-30

MS/MS Server/Cluster Solution: PEAKS Online 2.0 Release

Bioinformatics Solutions Inc, (BSI) producer of the highly accredited, globally popular PEAKS peptide mass spectrometry software, announced today its latest server/cluster solution, PEAKS Online 2.0. PEAKS gives greater coverage and confidence -- a more complete understanding of protein samples -- in one shot, using renowned de novo sequencing and protein identification algorithms. Ideal as a shared resource, this latest release of PEAKS Online, the high throughput webserver/cluster, now includes industry grade security and user management. System administrators can empower users and research groups to share resources without compromising security. PEAKS Online provides a forum for efficient collaboration. Free trial users can process multiple tests at once by harnessing the powerful PEAKS public server. Load in a private or public database and see the results on your own data using built-in and customizable enzymes and modifications.

Be among the first to investigate this new tool at no charge. Sign up for PEAKS Online at www.bioinfor.com/peaksonline. To read RAW data, inChorus (automatically compare results with Mascot, Sequest, X!Tandem, etc), manual de novo sequences or find homologous peptides using SPIDER, connect PEAKS Client to PEAKS Online.

2007-07-10

PEAKS Studio 4.5 (release)

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced, today, their much anticipated release of PEAKS 4.5 for peptide mass spectrometry analysis. PEAKS, known for its leadership role in de novo sequencing (sequencing of peptides not present in any database) is once again guiding tandem mass spectrometry researchers into in a new era of data analysis through sequence reconstruction. Accurate sequence reconstruction is performed by the built in SPIDER tool, which has been demonstrated to increase peptide findings by upwards of approximately 20%. Other cutting-edge enhancements to PEAKS help researchers to identify peptides using predicted retention time. PEAKS provides all of the necessary tools for superior peptide sequence derivation and protein identification from tandem MS/MS spectra - all within an intuitive graphical interface. PEAKS Studio 4.5 provides fast, accurate results for spectra from both sequenced and unsequenced organisms. Instrument Capabilities: Researchers are now fully capable of processing raw data, straight from their instruments (Agilent, Bruker, Shimadzu, Thermo and Waters to name a few). Visit www.bioinfor.com for more details.

2007-03-26

RAPTOR 4.1 release

BSI is proud to announce the release of RAPTOR 4.1 for Linux and Windows, the latest edition of protein threading software. RAPTOR is an innovative software tool designed to predict protein structure from protein sequence. Armed with unique integer programming algorithm, RAPTOR is capable of discovering remote structural homology for hard sequences and giving high quality prediction. As a participant in recent CASP's, RAPTOR has been consistently ranked in the top tier. In addition to the three threading methods proprietary to RAPTOR, the new version integrates PSI-BLAST for rapid identification of easy targets. A built in pipeline in RAPTOR 4.1 allows users to automatically run more rigorous threading techniques if necessary. RAPTOR 4.1 is your protein structure pipeline, right out of the box.

2006-11-24

PEAKS Studio 4.2 Release

Today, Waterloo software developers, Bioinformatics Solutions Inc. have launched their latest suite of proteomic software, PEAKS Studio 4.2. Among the preliminary benefits, de novo sequencing and protein identification, the latest advancements include faster processing time, simple reporting and improved exporting features. These are all provided in an attempt to reduce research time and increase accuracy. The software was released to the public following email notification of the upgrade to current customers. "Speed and efficiency were our goals for the new release," says Iain Rogers. "Our focus has resulted in users being able to not only view their results quickly, but in the format and order they prefer." An example is users can now view only publishable results: proteins identified by more than one high scoring peptides. Result reports can be filtered by a number of criteria (delta mass, proteins with X# of good hits inclusive and exclusive, etc). A simple report to summarize de novo sequencing on a whole run has been included. Further, the scans may now be sorted by scan number, mass, m/z, or retention time. The de novo options screen allows users to limit the number of variable modifications allowed in a proposed de novo sequence. In regards to exporting data to other locations PEAKS 4.2 allows use of spectra images, spectra with ions annotated, sequence-spectrum alignment, ion tables and error plots can now be exported in high resolution for printing. WYSIWYG (What You See Is What You Get) export of protein ID results, both from 'peptide view' and 'protein view' has been enabled. The embedded software, SPIDER, Software Protein Identifier, has been recalibrated for increased speed (several fold), along with accuracy. Perhaps the largest problem of the field of research is the multiple variations of file formats produced. In an attempt to create a uniform format, PEAKS supports HUPO's (Human Proteome Organization) proposed file format standard: mzData. Preliminary testers are raving about the new appearance of PEAKS and that is generally a good sign of the success in Mr. Rogers' focus into user coherence.

2006-09-06

RAPTOR 4.0 Release

Bioinformatics Solutions Inc. is proud to announce the release of RAPTOR 4.0 for Linux, the latest edition of protein threading software. RAPTOR is an innovative software tool designed to predict protein structure from protein sequence. Armed with unique integer programming algorithm, RAPTOR is capable of discovering remote structural homology for hard sequences and giving high quality prediction. As a participant in recent CASP's, RAPTOR has been consistently ranked in the top tier. RAPTOR 4.0 has a completely revamped GUI, which is considerably more interactive and easier for users to run sequences. The outputs are visualized vividly with consistent color scheme and users can easily understand the outputs. Users can try three different threading methods one by one in the GUI. The well designed configuration panel makes it possible for new users to set up RAPTOR in a few seconds. RAPTOR 4.0 has well designed interface and works seamlessly with Modeller. In addition, RAPTOR 4.0 can also generate ICM Pro input files. RAPTOR 4.0: Same effort, Even better output.

2006-07-26

BSI Partnership with Thermo Electron

A growing Canadian company, Bioinformatics Solutions Inc, specializing in mass spectrometry software, just confirmed a partnership with the world's largest Mass Spectrometer (instrument) manufacturers, Thermo Electron Inc., in West Palm Beach Florida, Tuesday.

VP of Business Development, Iain Rogers, was excited after presenting the recently released PEAKS Studio 4.0 software to Thermo's head Training and Support Representatives. PEAKS Studio 4.0 uses de novo (from scratch) sequencing and protein database search techniques to identify known and unknown peptides, for drug discovery.

"The presentation was only an hour long so my words had to resonate with their corporate identity. Thermo strives to make their mass spec solution the most capable, and is looking to specialists like BSI to complete the picture. Constructive discussion centered on how to integrate PEAKS de novo sequencing and sequence tag based protein characterization tools with Thermo's BioWorks package."

The recent good news for the Waterloo, Ontario based company is "a pleasant addition to the bustling new office," addressed Managing Director, Luosha Lu. "The recent release of PEAKS Online and PEAKS Q has been well received as have our latest versions of Raptor, PatternHunter and ProsepectPro. Bioinformatics Solutions is not shy to requests such as the Thermo partnership," Rogers reports, "BSI customized its software to such major brands as Thermo Electron, long before this opportunity came into scope."

2006-06-30

PEAKS Q: Software Launch

Bioinformatics Solutions Inc. have just released PEAKS Q, a Software for MS-based Quantification of Stable Isotope Labeled Peptides.

Several mass spectrometry-based stable isotope labeling technologies have been developed for global proteome profiling. These include methods for in vivo labeling, such as 14N/15N and SILAC (Stable Isotope Labeling with Amino Acids in Cell Culture), and in vitro isotope labeling of target peptides at their N/C terminal or at specific residues. PEAKS-Q, was designed to automatically identify and quantify proteins from these isotope labeling experiments. The software is written in Java and includes an intuitive graphical user interface.

In preliminary testing, PEAKS Q has demonstrated to be robust and an easy to use software for quantification of peptides from mass spectrometry. Its protein quantification accuracy is well within experimental error, and significance of abundance changes between samples is easy to see. Inquires for a copy of the free beta version can be located on the PEAKS Software Download page.

2006-06-30

PEAKS Studio 4.0: Software Launch

Bioinformatics Solutions Inc. (BSI) is proud to announce the release of the much anticipated PEAKS Studio 4.0. The latest in de novo sequencing and protein identification software yielding accurate results fast. By automatically filtering out insufficient quality results before database searching users can get the most out of low resolution data. Further, an increase in coverage is obtained by using four search engines for protein identification, instead of just one.

A new Software Protein IDentifiER, SPIDER, has also been bundled with PEAKS Studio 4.0. This sequence tag based search tool confidently identifies peptides using the de novo sequences derived by PEAKS auto de novo sequencing. Users can find protein information even in unstudied organisms, or find sequence variation between samples. SPIDER differs from regular homology search tools in that it was designed to account for inherent de novo sequencing errors like: (I/L), (N/GG), (SAT/TAS).

2006-06-20

New HQ

Bioinformatics Solutions Inc. moved its headquarters to a new location to accommodate the addition of several new team members. The long awaited move sees BSI in a bright and spacious office at 204-470 Weber St. North, in Waterloo, Ontario, (N2L 6J2). Email, web servers and phone systems were all transferred smoothly, so interested parties may still reach us at through the usual channels.

2006-01-06

PEAKS Online available on internet

You can now try the renowned PEAKS de novo sequencing and protein ID software using your web browser. Bioinformatics Solutions Inc. has opened access to the PEAKS Online server cluster. With a few mouse clicks, researchers worldwide can use their web browsers to submit MS/MS data and view results in moments. PEAKS Online is the web version of PEAKS Studio that has been designed with high throughput data analysis in mind. MS/MS data analysis has never been this fast, accurate, and simple!

PEAKS Online is available to the public at: www.bioinfor.com/peaksonline

Non-registered users are only limited by the amount of data they can submit daily.

2005-12-16

PEAKS Online 1.1 released

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced their latest release of PEAKS Online. PEAKS Online is a auto de novo and protein identification software that works on a computer cluster for enhanced performance. On a cluster, PEAKS Online shares the processing of MS/MS data between multiple computers. This decreases the data analysis to a fraction of the stand-alone type computational time.

There is a big difference between the initial version and this one. The overall computation is at least 4 times faster due to changes in to both the auto de novo and protein ID algorithm's efficiency. A taxonomy feature borrowed from PEAKS Studio has been implemented in this new version. A new user defined PTM (Post-translational modification) customization tool has also been added to the data submission window. Other small changes to the GUI have been made based on our customer input.

We are convinced that our users will be impressed with the improvements found in PEAKS Online 1.1.

2005-11-23

PEAKS Studio v3.1 is released

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced their latest de novo sequencing and protein identification software, PEAKS 3.1 today.

This is the fastest PEAKS to date. PEAKS Studio 3.1 boasts an increase in speed as high as 400% with some MS/MS data. The algorithms for both protein identification and de novo sequencing have been improved. There is also an improvement in the overall accuracy of the results.

To indirectly improve the overall speed and accuracy of PEAKS Studio, the development team has included a taxonomy search feature. The taxonomy add-on allows our users to specify the taxonomy of the organism under study. This focuses the protein ID search to a small subset of proteins, which shortens the search time.

PEAKS has matured a great deal in the 4 years since its first release and version 3.1 adds a great deal to the overall performance and stability of the product.

2005-11-17

New BSI branch opens

Bioinformatics Solutions Inc. (BSI), an advanced bioinformatics software provider announced its opening of its new branch, Beijing Bioinformatics Solutions Inc. (Beijing BSI), in Beijing China. The new branch started operation in August 2005, and is physically located in Tsinghua University high-tech incubator.

BSI was founded in 2000 as a spin-off from the University of Waterloo. The headquarters of the company are near the University in Waterloo, Ontario, Canada. The company's renowned bioinformatics products include PEAKS for protein identification from mass spectrometry, PatternHunter for homology search, and Prospect/Raptor for protein structure prediction. Over one hundred reputable customers worldwide have subscribed BSI's products. The opening of its Beijing branch is regarded as a step further to become an international bioinformatics solution provider.

2005-09-30

BSI Launches a new web-site

Welcome to the new face of BSI. The site is now organized according to the solutions we offer (see left). We hope the new arrangement will help you find the information you were looking for much quicker.

But it's not just about our products; it's also about you, our users, and the community at large. We hope to provide a space for you to share your research and your oppinions about our software. In this way we can learn from eachother.

2005-06-06

PEAKS Studio v3.0 is released

Waterloo software developers, BSI (Bioinformatics Solutions Inc.) announced their latest de novo sequencing and protein identification software, PEAKS 3.0 today. PEAKS 3.0 boasts an advance in protein identification technique. BSI has developed a meta search protein identification tool called "inChorus protien ID". This allows researchers to cross check their findings automatically. PEAKS 3.0 launches other search tools and integrate the results from all searches. Iain Rogers, part of the research team at BSI expressed this feature as "Get the right answer in one shot."

PEAKS 3.0 also uses tandem mass spectrometry data to find peptide sequences with our without the aid of a database. PEAKS technology prides itself as being the fastest, most accurate auto de novo sequencing algorithm on the market. It provides a complete sequence for each peptide, confidence score on individual amino acid assignments, simple reporting for high-throughput analysis, and all the information a researcher needs for in depth investigation. PEAKS provides all of the tools necessary for superior peptide sequence derivation and protein identification from tandem MS spectra - all within an intuitive graphical interface. Complete with auto de novo sequencing, manual de novo sequencing and protein database searching technology, PEAKS Studio 3.0 provides fast, accurate results for spectra from both sequenced and unsequenced organisms.