000195433 001__ 195433
000195433 005__ 20181203023406.0
000195433 0247_ $$2doi$$a10.1021/pr400522h
000195433 022__ $$a1535-3893
000195433 02470 $$2ISI$$a000328231300018
000195433 037__ $$aARTICLE
000195433 245__ $$aProteome Digestion Specificity Analysis for Rational Design of Extended Bottom-up and Middle-down Proteomics Experiments
000195433 260__ $$bAmer Chemical Soc$$c2013$$aWashington
000195433 269__ $$a2013
000195433 300__ $$a12
000195433 336__ $$aJournal Articles
000195433 520__ $$aMass spectrometry (MS)-based bottom-up proteomics (BUP) is currently the method of choice for large-scale identification and characterization of proteins present in complex samples, such as cell lysates, body fluids, or tissues. Technically, BUP relies on MS analysis of complex mixtures of small, <3 kDa, peptides resulting from whole proteome digestion. Because of the extremely high sample complexity, further developments of detection methods and sample preparation techniques are necessary. In recent years, a number of alternative approaches such as middle-down proteomics (MDP, addressing up to 15 kDa peptides) and top-down proteomics (TDP, addressing proteins exceeding 15 kDa) have been gaining particular interest. Here we report on the bioinformatics study of both common and less frequently employed digestion procedures for complex protein mixtures specifically targeting the MDP approach. The aim of this study was to maximize the yield of protein structure information from MS data by optimizing peptide size distribution and sequence specificity. We classified peptides into four categories based on molecular weight: 0.6-3 (classical BUP), 3-7 (extended BUP), 7-15 kDa (MDP), and >15 kDa (TDP). Because of instrumentation-related considerations, we first advocate for the extended BUP approach as the potential near-future improvement of BUP. Therefore, we chose to optimize the number of unique peptides in the 3-7 kDa range while maximizing the number of represented proteins. The present study considers human, yeast, and bacterial proteomes. Results of the study can be further used for designing extended BUP or MDP experimental workflows.
000195433 6531_ $$amass spectrometry
000195433 6531_ $$aMS
000195433 6531_ $$aproteomics
000195433 6531_ $$amiddle-down proteomics
000195433 6531_ $$atop-down proteomics
000195433 6531_ $$abottom-up proteomics
000195433 700__ $$0245624$$g218425$$uEcole Polytech Fed Lausanne, Biomol Mass Spectrometry Lab, CH-1015 Lausanne, Switzerland$$aLaskay, Uenige A.
000195433 700__ $$uRussian Acad Sci, Inst Energy Problems Chem Phys, Moscow 119334, Russia$$aLobas, Anna A.
000195433 700__ $$0246379$$g222806$$uEcole Polytech Fed Lausanne, Biomol Mass Spectrometry Lab, CH-1015 Lausanne, Switzerland$$aSrzentic, Kristina
000195433 700__ $$uRussian Acad Sci, Inst Energy Problems Chem Phys, Moscow 119334, Russia$$aGorshkov, Mikhail V.
000195433 700__ $$aTsybin, Yury O.$$g174689$$0240220
000195433 773__ $$j12$$tJournal Of Proteome Research$$k12$$q5558-5569
000195433 909C0 $$xU11424$$0252074$$pLSMB
000195433 909CO $$pSB$$particle$$ooai:infoscience.tind.io:195433
000195433 917Z8 $$x148230
000195433 917Z8 $$x148230
000195433 937__ $$aEPFL-ARTICLE-195433
000195433 973__ $$rREVIEWED$$sPUBLISHED$$aEPFL
000195433 980__ $$aARTICLE