Abstract
Automated liquid chromatography tandem mass spectrometry (LC-MS/MS) is a well-established technique for identification of components from complex mixtures in shotgun proteomics experiments. Approaches involving the use of matrix-assisted laser desorption/ionization mass spectrometry (LC-MALDI-MS/MS) comprise the preparation of protein extracts, their enzymatic digestion, the separation of the resulting peptides by nanoscale liquid chromatography coupled to a collector that deposits the microfractions onto a MALDI plate, and finally the mass spectrometry analysis of the fractions. Using an LC-MALDI strategy, the rate of the collection of MS/MS data is decoupled from the chromatographic separation, thus allowing high-quality data which are often complementary to electrospray ionization (LC-ESI-MS/MS) techniques.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Wolters DA, Washburn MP, Yates JR 3rd (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73:5683–5690
Yang Y, Zhang S, Howe K, Wilson DB, Moser F, Irwin D, Thannhauser TW (2007) A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics. J Biomol Tech 18:226–237
Mueller DR, Voshol H, Waldt A, Wiedmann B, Van Oostrum J (2007) LC-MALDI MS and MS/MS–an efficient tool in proteome analysis. Subcell Biochem 43:355–380
Mateos J, Lourido L, Fernandez-Puente P, Calamia V, Fernandez-Lopez C, Oreiro N, Ruiz-Romero C, Blanco FJ (2012) Differential protein profiling of synovial fluid from rheumatoid arthritis and osteoarthritis patients using LC-MALDI TOF/TOF. J Proteome 75:2869–2878
Fernandez-Puente P, Mateos J, Fernandez-Costa C, Oreiro N, Fernandez-Lopez C, Ruiz-Romero C, Blanco FJ (2011) Identification of a panel of novel serum osteoarthritis biomarkers. J Proteome Res 10:5095–5101
Calamia V, Rocha B, Mateos J, Fernandez-Puente P, Ruiz-Romero C, Blanco FJ (2011) Metabolic labeling of chondrocytes for the quantitative analysis of the interleukin-1-beta-mediated modulation of their intracellular and extracellular proteomes. J Proteome Res 10:3701–3711
Bodnar WM, Blackburn RK, Krise JM, Moseley MA (2003) Exploiting the complementary nature of LC/MALDI/MS/MS and LC/ESI/MS/MS for increased proteome coverage. J Am Soc Mass Spectrom 14:971–979
Zhen Y, Xu N, Richardson B, Becklin R, Savage JR, Blake K, Peltier JM (2004) Development of an LC-MALDI method for the analysis of protein complexes. J Am Soc Mass Spectrom 15:803–822
Acknowledgement
Our work is supported by grants from Fondo Investigación Sanitaria-Spain (CP09/00114, PI11/02397, PI12/00329) and Secretaría I + D + I Xunta de Galicia (10CSA916058PR). J. Mateos (CA11/00050) and P. Fernández-Puente (CA09/00458) are supported by Fondo Investigación Sanitaria-Spain. C. Ruiz-Romero is supported by the Miguel Servet program from Fondo Investigación Sanitaria-Spain (CP09/00114).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this protocol
Cite this protocol
Fernández-Puente, P., Mateos, J., Blanco, F.J., Ruiz-Romero, C. (2014). LC-MALDI-TOF/TOF for Shotgun Proteomics. In: Martins-de-Souza, D. (eds) Shotgun Proteomics. Methods in Molecular Biology, vol 1156. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0685-7_2
Download citation
DOI: https://doi.org/10.1007/978-1-4939-0685-7_2
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-0684-0
Online ISBN: 978-1-4939-0685-7
eBook Packages: Springer Protocols