Protein Metrics


Protein Metrics is led by a team with world-class expertise in business development, algorithm design, and software engineering grounded in fundamental understanding of protein science and biopharma development. With this group’s vision, the company is creating software tools for protein characterization to match the rapidly innovating hardware tools created by the leading scientific instrument companies.

Outside Directors

Scientific Advisors and Collaborators

News & Announcements

We release products every quarter that advance protein characterization workflows. Our customers frequently publish groundbreaking research using our products. Please visit here often for our latest updates and news.

Events & Webinars

We create world-class learning events, and connect with our customers at key industry trade shows. Please sign up, or stop by and see us.


2nd Australasian Glycoscience Symposium

WHEN: 16 – 17 September

WHERE:  Adelaide, Australia

WHAT:  Protein Metrics is a sponsor

CASSS Mass Spec 2019

DATE: Sept. 17 – 20, 2019

WHERE: Palmer House, Chicago IL

WHAT: Technical Seminar on Friday, Sept.20, 11:45 AM, features Dr. Göran Hübner, Boehringer Ingelheim.
PLUS: See 5 new posters from Protein Metrics and our partners

Protein Metrics 2019 European Users Meeting

SAVE THE DATE: 1 and 2, October
WHERE: Hotel La Barcarolle, Geneva

More Information

PEGS Europe 2019

DATE:  18-22 November

BOOTH: 325

WHERE:  Lisboa, Portugal

CONTACT:  Pierre Allemand,


Register for our live webinar: PTM Analysis – How to Marry Speed and Confidence in R&D

DATE: September 17, 2019
PRESENTERS: Jon Reed, Boehringer Ingelheim Pharmaceuticals and St John Skilton, Protein Metrics

Register for our live webinar: Automation of Glycan and Peptide Mapping – Leveraging Software to Improve Efficiency and Quality

DATE: September 4, 2019
PRESENTERS: Thomas Wesley Powers, Pfizer and Michelle English, Protein Metrics

Register: An Implementation of Vendor-Neutral Multi-Attribute Method (MAM)

DATE / TIME: On-Demand Webinar

PRESENTER:  Ben Niu, Scientist / Characterization Lead, MedImmune


Register: How to Advance Your Host Cell Protein Analysis with Mass Spectrometry

DATE / TIME: On-Demand Webinar

PRESENTERS:  Dr. Kevin Van Cott, University of Nebraska and Dr. Ilker Sen, Protein Metrics

Register: Driving Efficiency in Pre-Clinical Development with Automated Mass-Spectrometry Analysis

DATE/TIME:  On-Demand Webinar

PRESENTERS:  Dr Hirsh Nanda, Janssen and Dr Eric Carlson, Protein Metrics


Customer Testimonials

We collaborate with customers all over the world, helping them achieve their research goals and utilizing their input for our product development. We’re proud to share their successes here.

“With the 64bit Byonic and Java, our searches are lightening fast compared to how they were prior!. You all are awesome! Just wanted to say thanks again for your help!”

Lawrie Gainey
Research Specialist, Oklahoma State University

“This is the workflow/software that I have been wanting for over a decade. I just completed a large comparability study for a glycoprotein that has both N-linked and O-linked glycosylation. Compared to what my workflow used to be with the software my MS vendor sold, the process with Byonic™Byologic®, and ByoMap™ was much more efficient and straightforward.  Byologic gives the user ready access to all pertinent information for each peptide, and ByoMap helps me generate informative comparability chromatograms very quickly.  Also, in a project like this, I spend a great deal of time writing reports for people who are not necessarily MS-savvy.  Once I learned how to use and customize reports in Byologic and ByoMap, that process was streamlined as well.”

Kevin Van Cott, Ph.D.
Associate Professor, University of Nebraska, Lincoln, Chemical and Biomolecular Engineering

Byos enabled our lab to characterize and report on sets of candidates in parallel, reducing analytical time for clone selection by 20-30%, and substantially improving our ability to identify robust candidates for development.”

Hirsh Nanda, Ph.D.
Associate Director and Team Manager, Cell and Developability Sciences, Janssen Pharmaceuticals

“With Byologic® I replaced six different analytical LC/MS Peptide map methods (six analysts doing six methods) with one MS method.  We transferred it to the High Throughput Screening group.  They can run that one method faster than it used to take one analyst to run an individual method, and we can generate and ask questions much more quickly.

Using Protein Metrics software, we can also run cell-culture samples directly in days.  Prior to implementing their software, it took us six months to send samples to purification and then analyze them.”

Matt Traylor, Ph.D.
Associate Director, Analytical Development, Shire

“Protein Metrics software is a powerful tool for analyzing glycosylation and other PTMS.  Their software greatly alleviates the mass spec analysis bottleneck.”

Wilson Phung
Scientific Researcher, Genentech

“I really like the Protein Metrics software. It helped us to make advances that we may not have been able to with other software. It identified protein impurities that we couldn’t make with other software. I was impressed with the auto reporting features and search engine. We realized cost savings and were able to reallocate resources. We can now get deeper into our to data to find what we’re looking for. The people are really great to deal with – Eric and the team – fantastic, we get a very good response from them.”

Mimi Roy, Ph.D.
Sr. Director, Analytical DevelopmentAmerican biotech focused on enzyme replacement therapies

“With Protein Metrics’ analytical software, we are providing our clients access to enhanced capabilities by partnering with experts in related biotherapeutic areas.”

Haddon Goodman, M.S.
Vice President, Corporate Development, Protea Biosciences

“Our mission is to push science forward as much as we can, and Protein Metrics software helps us accomplish this.  Particularly, we find their Intact Mass™ software simple to use but also powerful and flexible, so we expect to utilize it further.”

Yury Tsybin, Ph.D.
CEO, Spectroswiss

“I wanted to let you know that Byonic™ is fantastic. I am very impressed; it’s the best search engine I have ever used. I have some rock solid head-to-head comparisons vs. other protein analysis software.”

Laurence Brill, Ph.D.
Senior Scientist, Intertek

“Protein Metrics’ Byonic™ software is a powerful proteomics tool. Relative to other search engines such as Sequest and Mascot, we have observed a significant gain in speed and overall peptide identifications. Byonic is especially powerful in identifying isobarically tagged peptides and peptide PTMs, such as glycosylation. Byonic has become the primary tool for peptide identification in our lab and provides our research collaborators with the most robust data sets.”

Chris Adams, Ph.D.
Director of Proteomics, Stanford University Mass Spectrometry, Stanford University

Byonic™ very quickly became the search engine of choice in my lab as it handles CAD, HCD and ETD data equally well and superior to other search engines we have used. We especially came to rely on the precision with which Byonic identifies PTMs and even unanticipated modifications and sequence variants. Several projects in my lab depend on Byonic’s Wildcard search that allows us to place a large mass window on a specific or all amino acids without decreasing the sensitivity of our search. Using the wildcard modification in combination with Byonic’s integrated top down search became a game changer for our lab. We are now routinely characterizing complex mixtures of 8kDa proteins from organisms with incomplete database in a top down manner without fractionation or sub-digestion. Not only do we identify exact matches to RNA-Seq data, but we also identify numerous additional sequence variants and PTMs all top down. The exhaustive annotation of Byonic makes it incredibly easy to rapidly validate the identifications. Truly Byonic is the one-stop-shop for exhaustive protein characterization from top to bottom.”

Beatrix Ueberheide, Ph.D.
Assistant Professor, Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center

“…[Protein Metrics] is quietly writing the best shotgun proteomics software I have ever seen….”

Benjamin Orsburn, Ph.D.
Senior Application Scientist, Proteomics News Blog

“For us, Byonic™ has opened new windows in the study of cardiovascular disease.”

Manuel Mayr M.D., Ph.D.
Professor of Cardiovascular Proteomics, King’s College London

“Protein Metrics’ Byonic™ has changed the way we evaluate our data and even do our up front experiments. The ability of this program to address mass spectra of glycopeptides directly is a Game Changer.  No other program that I am aware of, and we have used many, can compete for assigning glycopeptides. This is not to mention the speed of the searches that are phenomenal….Byonic runs a search faster looking for multiple modifications than the previous program we were using allowing for no modifications!”

Lance Wells, Ph.D.
Prof. Biochem. and Mol. Biol., University of Georgia

“It’s great for our field to have a single search engine, Byonic™ which excels at all the different proteomics methods — data-dependent, data-independent, bottom-up, top-down, glycoproteins, and phosphoproteins.”

Michael MacCoss, Ph.D.
Assoc. Professor of Genome Sciences, University of Washington School of Medicine

Byonic™ has enabled us to evaluate complex tissues and biofluids at the glycopeptide level, allowing simultaneous glycan composition and peptide identification determinations. Using Byonic in our analytical workflow has greatly facilitated evaluation of known key biomarker glycoproteins like PSA, and also improved our ability to discover new cancer biomarker candidates.  Additionally, the Protein Metrics staff have been exceptionally helpful in assisting with any software and data analysis questions that we have had, as well as troubleshooting different experimental approaches.”

Richard Drake, Ph.D.
Professor and Director, Medical University of South Carolina Proteomics Center

Byonic™and Preview™ have become integral tools for our discovery proteomics pipeline.  Searches are rapid, customizable, statistically validated and highly informative.  One of the best aspects is the ability to interface with the vendor and its programmers directly for advice on configurations and for collaborative implementation of new features.”

Mark Flory, Ph.D.
Principal Scientist, Igenica, Inc.

“In my research, we are always looking for unexpected modifications to our proteins.  Protein Metrics’ Byonic™ software has allowed us to find modifications that we haven’t even considered before.  With other software products we have used we were only able to find what we already knew was there.”

Joshua S. Sharp, Ph.D.
Assistant Research Scientist, University of Georgia

“…[Preview™ quickly evaluates your RAW data and gives you an idea of how you should be setting up your searches…this software is very very fast.”

Benjamin Orsburn, Ph.D.
Senior Application Scientist, Proteomics News Blog


We’ve built a powerful suite of products from groundbreaking patents that we either own or have exclusively licensed. As we continue to push protein characterization, we have an ongoing series of additional pending patents and patent applications. Some of our patents include:


  • US 10,510,521 B2 – Interactive analysis of mass spectrometry data
  • US 10,354,421 B2 – Apparatus and methods for annotated peptide mapping
  • US 10,319,573 B2 – Methods and apparatuses for determining the intact mass of large molecules from mass spectrographic data
  • US 10,199,206 – Interactive analysis of mass spectrometry data
  • US 9,859,917 B2 – Enhanced Data Compression For Sparse Multidimensional Ordered Series Data
  • US 9,640,376 – Interactive analysis of mass spectrometry data
  • US 9,571,122 – Enhanced data compression for sparse multidimensional ordered series data
  • US 9,385,751 – Enhanced data compression for sparse multidimensional ordered series data
  • US 8,108,153 – Method, apparatus, and program product for creating an index into a database of complex molecules
  • US 7,979,258 – Self-calibration of mass spectra using robust statistical methods
  • US  7,283,937 – Method, apparatus, and program product for distinguishing valid data from noise data in a data set
  • US 7,741,126 – Automated Identification of Carbohydrates in Mass Spectra
  • US 7,429,727 – Method, apparatus, and Program Product for Quickly Selecting Complex Molecules From a Database of Molecules
  • US 7,402,438 – Automated Identification of Carbohydrates in Mass Spectra
  • US 7,297,940 – Method, Apparatus, and Program Product for Classifying Ionized Molecular Fragments
  • US 2010-0124785 A1 – Wild-Card-Modification Technique for Peptide Identification
  • US 20160-267220 A1 – Apparatuses and methods for annotated peptide mapping


We’re always looking for talented professionals to join our team. If you’re interested in building cutting-edge scientific software to clear the skies and advance human health, please email us at

Email us now


  • Software Engineer / Senior Software Engineer
  • Software Configuration Management Engineer (DevOps)
  • Software and Algorithm Engineer
  • Customer Success Scientist