@inbook{556a9ac20e434c91b34681f80c35b1cf,
title = "Proteomic Database Search and Analytical Quantification for Mass Spectrometry",
abstract = "Technological development and the ever-increasing complexity of proteomic profiling studies requires automated tools for tandem mass spectra interpretation. The analysis of various methods used for accurate and sensitive quantitation adds another layer of complexity. Therefore, investigators need a more in-depth understanding of database searches and the calculation of statistical significance in order to find a proper bioinformatics approach for their study. In this chapter, we review tools and procedures that have been developed in two decades of collective experience in the proteomics field. However, the field is still in dynamic expansion thus intention of this chapter is to provide readers with background for reading about the newest tools and approaches developed for database searches.",
keywords = "Analytical quantification, Database search, Mass spectrometry data searches, Post-database search data processing, Protein databases, Search engines",
author = "M. Wojtkiewicz and J. Wiederin and P. Ciborowski",
note = "Funding Information: PhosphoSitePlus (PSP) ( www.phosphosite.org ) is an online resource for protein modifications, such as phosphorylation, acetylation, ubiquitination and methylation. The National Institutes of Health (NIH), National Cancer Institute (NCI), National Institute on Alcohol Abuse and Alcoholism (NIAAA) and National Institute of General Medical Sciences (NIGMS) provide grant funding to Cell Signaling Technology (CST) for maintaining the website. The major goal of PSP is to provide a comprehensive systems biology website where researchers can retrieve information and have tools to study posttranslational modifications in the context of biological regulation, subcellular location, disease, etc. PSP is routinely modified and updated to stay relevant with rapidly evolving proteomic technology and data [5] . Funding Information: Swiss-Prot, created in 1986, is a biological database of protein sequences that is manually curated, or reviewed and edited by experts. For that reason, Swiss-Prot provides reliable protein sequences associated with annotation with a minimal level of redundancy. In 2002, collaboration between the Swiss Institute of Bioinformatics, the European Bioinfomatics Institute and the Protein Information Resource (PIR), funded by the National Institutes of Health, formed the UniProt consortium, combining Swiss-Prot and its automatically curated supplement TrEMBL (the Protein Information Resource protein database), creating the most comprehensive catalog of protein information. An updated UniProtKB/Swiss-Prot protein knowledgebase release and statistics can be found at http://web.expasy.org/docs/relnotes/relstat.html . Publisher Copyright: {\textcopyright} 2016 Elsevier B.V. All rights reserved.",
year = "2016",
month = mar,
day = "22",
doi = "10.1016/B978-0-444-63688-1.00011-2",
language = "English (US)",
isbn = "9780444636881",
pages = "193--210",
booktitle = "Proteomic Profiling and Analytical Chemistry",
publisher = "Elsevier Inc.",
}