The Pattern Recognition in Bioinformatics (PRIB) meeting was established in 2006 under the auspices of the International Association for Pattern Recognition (IAPR) to create a focus for the development and application of pattern recognition techniques in the biological domain. PRIB's aim to explore the full spectrum of pattern recognition application was re?ected in the breadth of techniquesrepresented in this year's subm- sions and in this book. These range from image analysis for biomedical data to systems biology. We werefortunatetohaveinvitedspeakersofthehighestcalibredeliveringkeynotes at the conference. These were Pierre Baldi (UC Irvine), Alvis Brazma (EMBL-EBI), GunnarRats .. ch(MPITubi .. ngen)andMichaelUnser(EPFL).Weacknowledgesupportof theEUFP7NetworkofExcellencePASCAL2forpartiallyfundingtheinvitedspeakers. Immediately prior to the conference, we hosted half day of tutorial lectures, while a special session on "Machine Learningfor IntegrativeGenomics" was held immediately after the main conference.Duringthe conference,a poster session was heldwith further discussion. Wewouldlikeonceagaintothankalltheauthorsforthehighqualityofsubmissions, as well as Yorkshire South and the University of Shef?eld for providing logistical help in organizing the conference. Finally, we would like to thank Springer for their help in assembling this proceedings volume and for the continued support of PRIB.

New insights into modern medicine and systems biology are enabled by innovative protocols and advanced technologies in mass spectrometry-based proteomics. This volume details new pipelines, workflows, and ways to process data that allow for new frontiers in proteomics to be pushed forward. With applications to biomarker discovery, interactions between proteins, between biological systems, dynamics of post-translational modifications among others, new protocols have been developed and iteratively refined to probe the endless complexity of the proteome in ever greater details. This volume deals with methods for data dependent and data independent mass spectrometry analyses. Valuable, first-hand information is provided from designing experiments, sample preparation and analysis, exploitation of public datasets and carrying out reproducible data pipelines, using modern computational tools such as Galaxy or Jupyter. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Mass Spectrometry of Proteins: Methods and Protocols aims to ensure successful results in the further study of this vital field.