Publications
Laura Perez Paneda, Tereza Kadava, Tatiana M. Shamorkina, Douwe Schulte, Patrick Pribil, Sibylle Heidelberger, Allison Michele Narlock-Brand, Steven M. Yannone, Joost Snijder, and Albert J.R. Heck
AUTHORS
JOURNAL
Deep coverage and extended sequence reads obtained with a single archaeal protease expedite de novo protein sequencing by mass spectrometry
High Throughput Proteomics
Antibody Sequencing
March 11, 2026
ABSTRACT
Steven M. Yannone, Vikas Tuteja, Olena Goleva, Donald Y. M. Leung, Aleksandr Stotland, Angel J. Keoseyan, Nathan G. Hendricks, Sarah Parker, Jennifer E. Van Eyk, and Simion Kreimer
AUTHORS
JOURNAL
Toward Real-Time Proteomics: Blood to Biomarker Quantitation in under One Hour
High Throughput Proteomics
Difficult Proteins
March 20, 2025
ABSTRACT
Biomarker Discovery
Maxwell C. McCabe, Varun Gejji,, Adam Barnebey , Gary Siuzdak , Linh Truc Hoang , Truc Pham , Keira Y. Larson , Anthony J. Saviola, Steven M. Yannone, Kirk C. Hansen
AUTHORS
JOURNAL
From volcanoes to the bench: Advantages of novel hyperthermoacidic archaeal proteases for proteomics workflows
How To Use
Difficult Proteins
October 30, 2023
ABSTRACT
Lauren G. Poole, Lauren R. Schmitt, Anthony Schulte, Dafna J. Groeneveld, Holly M. Cline, Yaqiu Sang, Woosuk S. Hur, Alisa S. Wolberg, Matthew J. Flick, Kirk C. Hansen, James P. Luyendyk
AUTHORS
JOURNAL
Altered fibrinogen γ-chain cross-linking in mutant fibrinogen-γ mice drives acute liver injury
April 3, 2023
ABSTRACT
Δ5
Difficult Proteins
Biomarker Discovery
Sean Reichard
AUTHOR
SOURCE
CinderBio Derives New Enzyme From Yellowstone Hot Springs
November 11, 2015
Industrial
Berkeley startup CinderBio has engineered highly heat- and acid-resistant enzymes derived from Yellowstone National Park's extreme bacteria. These unique enzymes can replace harsh chemicals in industrial processes like food equipment cleaning. In successful creamery trials, they reduced water use by 30% while cleaning faster and more effectively.
Application Notes
How To Use
Determination of unknown PTMs and increased protein sequence coverage from high temperature acidic enzyme digests
Natalie Korkola, Bioinformatics Solutions Inc., Waterloo, Canada
It is important to consider the appropriate PTMs in proteomics searches, to obtain the most complete data possible. However, it is not always known which PTMs to select in advance of a search. In particular, atypical digestion conditions such as the high temperatures and low pH used for hyperthermoacidic archaeal (HTA) enzyme digestions may produce different PTMs during sample preparation than those produced during a typical tryptic digest. Here, the PEAKS PTM algorithm, part of the PEAKS Studio 13 software package, is used to determine the differences in PTMs between a tryptic digest and HTA digests. This approach yielded an 8% increase in protein ID’s forHTA-protease data and boosted the number of protein ID’s seen only with HTA digests from 91 to 248 proteins.
Full de novo sequence coverage and complete automatic assembly of an IgG using a single hyperthermoacidic archaeal enzyme and PEAKS AB 3.5
Natalie Korkola, Bioinformatics Solutions Inc. Waterloo, Canada
Antibody sequencing usually requires performing multiple time-consuming, orthogonal enzyme digests for adequate sequence coverage and assembly. In this application note, complete de novo sequencing coverage and automatic assembly of human IgG is achieved using a single enzyme digest and PEAKS AB 3.5. The novel use of a single hyperthermoacidic archaea enzyme for complete, accurate sequence coverage is unprecedented.
Antibody Sequencing
Conference Posters & Presentations
ASMS 2025 Posters
Automatable One-Step 5-minute Sample Preparation with Novel Hyperthermoacidic Proteases Generates Novel Protein ID's and Sequence
Biomarker Discovery
Difficult Proteins
Antibody Sequencing
Hot de novo Antibody Sequencing: one protease, one run, massively redundant reads covering all hypervariable regions
How To Use
Unleashing Krakatoa: Assessing a Novel Alternative Enzyme for MS-Based Proteomics
US HUPO 2025 Presentations & Posters
Biomarker Discovery
Presentation
Rapid and Complete Biopharmaceutical Sequencing using a Tunable Hyperthermoacidic Archaeal Protease
Difficult Proteins
How To Use
High Throughput Proteomics
Difficult Proteins
Poster
From Volcanoes to the Bench: Advantages of Hyperthermoacidic Archaeal Proteases for Proteomics Workflows