Protein identification by 3D OrbiSIMS to facilitate in situ imaging and depth profiling

Nature Communications
Anna M KotowskaDavid J Scurr

Abstract

Label-free protein characterization at surfaces is commonly achieved using digestion and/or matrix application prior to mass spectrometry. We report the assignment of undigested proteins at surfaces in situ using secondary ion mass spectrometry (SIMS). Ballistic fragmentation of proteins induced by a gas cluster ion beam (GCIB) leads to peptide cleavage producing fragments for subsequent OrbitrapTM analysis. In this work we annotate 16 example proteins (up to 272 kDa) by de novo peptide sequencing and illustrate the advantages of this approach by characterizing a protein monolayer biochip and the depth distribution of proteins in human skin.

References

Oct 3, 1998·Acta Crystallographica. Section D, Biological Crystallography·K LimM L Pusey
Mar 5, 2002·Nature Biotechnology·Peter Mitchell
Mar 1, 2003·Nature Biotechnology·Peter Mitchell
Apr 29, 2004·Journal of Proteome Research·Pierre ChaurandRichard M Caprioli
Sep 2, 2004·Nature Reviews. Molecular Cell Biology·Hanno Steen, Matthias Mann
Mar 29, 2008·Analytical and Bioanalytical Chemistry·Falk BernsmannHubert Gnaser
Feb 4, 2010·Analytical Chemistry·Santiago Solé-DomènechPeter Sjövall
Mar 9, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·V I TimofeevI P Kuranova
Jul 12, 2011·Analytical Biochemistry·Kathleen HofmanSusan Marshall
Aug 16, 2012·Biointerphases·Daniel J Graham, David G Castner
Sep 21, 2013·Journal of the American Society for Mass Spectrometry·Wei RaoDavid A Barrett
Jan 7, 2015·ACS Applied Materials & Interfaces·James BaileyDavid J Scurr
Jan 24, 2015·Science·Mathias UhlénFredrik Pontén
Feb 24, 2015·Molecular BioSystems·Seungjin NaJoseph Kwon
Jul 22, 2015·Molecular & Cellular Proteomics : MCP·Nicholas M RileyJoshua J Coon
Jul 20, 2017·Proceedings of the National Academy of Sciences of the United States of America·Ngoc Hieu TranMing Li
Apr 3, 2018·Journal of Mass Spectrometry : JMS·Klaudia I KocurekHelen J Cooper
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 27, 2018·Current Opinion in Chemical Biology·Daniel J RyanRichard M Caprioli
Feb 7, 2019·ACS Applied Materials & Interfaces·Giuseppe Di PalmaPaula M Mendes
Mar 20, 2019·International Journal of Pharmaceutics·Nichola J StarrDavid J Scurr
Apr 16, 2020·Biointerphases·Jin Gyeong SonTae Geol Lee

❮ Previous
Next ❯

Citations

Mar 4, 2021·Journal of the American Society for Mass Spectrometry·Michael J TaylorChristopher R Anderton
May 28, 2021·The Analyst·Yiheng MaoRuijun Tian
May 29, 2021·Mass Spectrometry Reviews·Jessica L NickersonAlan A Doucette
May 13, 2021·Annual Review of Analytical Chemistry·Tobias Weidner, David G Castner

❮ Previous
Next ❯

Methods Mentioned

BETA
transmission electron microscopy
X-ray
biosensors
electron transmission microscopy

Software Mentioned

ThermoFisher Tune
Xcalibur
SurfaceLab
MATLAB
Thermo Xcalibur
PyMol TM
CompleteEASE
ChemDraw Professional
IonToF SurfaceLab
Orbitrap

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.