Identification and Quantification of Proteoforms by Mass Spectrometry

Leah V Schaffer; Robert J Millikin; Rachel M Miller; Lissa C Anderson; Ryan T Fellers; Ying Ge; Neil L Kelleher; Richard D LeDuc; Xiaowen Liu; Samuel H Payne; Liangliang Sun; Paul M Thomas; Trisha Tucholski; Zhe Wang; Si Wu; Zhijie Wu; Dahang Yu; Michael R Shortreed; Lloyd M Smith

doi:10.1002/pmic.201800361

Identification and Quantification of Proteoforms by Mass Spectrometry

Proteomics. 2019 May;19(10):e1800361. doi: 10.1002/pmic.201800361.

Authors

Leah V Schaffer¹, Robert J Millikin¹, Rachel M Miller¹, Lissa C Anderson², Ryan T Fellers³, Ying Ge^{1

4}, Neil L Kelleher^{3

5}, Richard D LeDuc³, Xiaowen Liu^{6

7}, Samuel H Payne⁸, Liangliang Sun⁹, Paul M Thomas³, Trisha Tucholski¹, Zhe Wang¹⁰, Si Wu¹⁰, Zhijie Wu¹, Dahang Yu¹⁰, Michael R Shortreed¹, Lloyd M Smith¹

Affiliations

¹ Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
² Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Tallahassee, FL, 32310, USA.
³ Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA.
⁴ Department of Cell and Regenerative Biology and Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
⁵ Department of Chemistry and Molecular Biosciences and the Division of Hematology and Oncology, Northwestern University, Evanston, IL, 60208, USA.
⁶ Department of BioHealth Informatics, Indiana University-Purdue University, Indianapolis, IN, 46202, USA.
⁷ Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
⁸ Department of Biology, Brigham Young University, Provo, UT, 84602.
⁹ Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
¹⁰ Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.

Abstract

A proteoform is a defined form of a protein derived from a given gene with a specific amino acid sequence and localized post-translational modifications. In top-down proteomic analyses, proteoforms are identified and quantified through mass spectrometric analysis of intact proteins. Recent technological developments have enabled comprehensive proteoform analyses in complex samples, and an increasing number of laboratories are adopting top-down proteomic workflows. In this review, some recent advances are outlined and current challenges and future directions for the field are discussed.

Keywords: bioinformatics; mass spectrometry; proteoform; proteoform family; top-down proteomics.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Amino Acids / analysis*
Animals
Computational Biology
Electrophoresis, Capillary
Humans
Mass Spectrometry*
Programming Languages
Protein Processing, Post-Translational*
Proteome / analysis*
Proteomics / methods*
Reproducibility of Results
Software

Substances

Amino Acids
Proteome

Abstract

Publication types

MeSH terms

Substances

Grants and funding