title: A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.
abstract: Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
authors.forename: Juan D
authors.initials: JD
authors.lastname: Chavez
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
authors.forename: Jimmy K
authors.initials: JK
authors.lastname: Eng
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
authors.forename: Devin K
authors.initials: DK
authors.lastname: Schweppe
authors.affiliation: Boyce Thompson Institute for Plant Research, Ithaca, NY, United States of America.|USDA-Agricultural Research Service, Ithaca, NY, United States of America.|Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States of America.
authors.forename: Michelle
authors.initials: M
authors.lastname: Cilia
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America.
authors.forename: Keith
authors.initials: K
authors.lastname: Rivera
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
authors.forename: Xuefei
authors.initials: X
authors.lastname: Zhong
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
authors.forename: Xia
authors.initials: X
authors.lastname: Wu
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Terrence
authors.initials: T
authors.lastname: Allen
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Moshe
authors.initials: M
authors.lastname: Khurgel
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Athanasios
authors.initials: A
authors.lastname: Lampropoulos
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Mårten
authors.initials: M
authors.lastname: Larsson
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Shuvadeep
authors.initials: S
authors.lastname: Maity
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Yaroslav
authors.initials: Y
authors.lastname: Morozov
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Wimal
authors.initials: W
authors.lastname: Pathmasiri
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Mathew
authors.initials: M
authors.lastname: Perez-Neut
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Coriness
authors.initials: C
authors.lastname: Pineyro-Ruiz
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Polina
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Post
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Rider
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Dorota
authors.initials: D
authors.lastname: Tokmina-Roszyk
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Katherine
authors.initials: K
authors.lastname: Tyson
authors.affiliation: Cold Spring Harbor Laboratory Proteomics Course 2016, Cold Spring Harbor, NY, United States of America.
authors.forename: Debora
authors.initials: D
authors.lastname: Vieira Parrine Sant'Ana
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America.
authors.forename: James E
authors.initials: JE
authors.lastname: Bruce
mesh_terms: D000818:Animals; D002417:Cattle; D003432:Cross-Linking Reagents / Q000737:chemistry*; D006367:HeLa Cells; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D020836:Protein Structure, Quaternary; D040901:Proteomics / Q000379:methods*; D012710:Serum Albumin, Bovine / Q000032:analysis* / Q000737:chemistry; D012984:Software
chemical_list: D003432:Cross-Linking Reagents; D012710:Serum Albumin, Bovine