Filtered By:
Specialty: Biochemistry

This page shows you your search results in order of relevance.

Order by Relevance | Date

Total 109397 results found since Jan 2013.

Sweet Emotion: The Role of Odor-induced Context in the Search Advantage for Happy Facial Expressions.
Abstract The current study investigated the extent to which the concurrent presentation of pleasant and unpleasant odors could modulate the perceptual saliency of happy facial expressions in an emotional visual search task. Whilst a search advantage for happy faces was found in the no odor and unpleasant odor conditions, it was abolished under the pleasant odor condition. Furthermore, phasic properties of visual search performance revealed the malleable nature of this happiness advantage. Specifically, attention towards happy faces was optimized at the start of the visual search task for participants presented wit...
Source: Chemical Senses - December 23, 2017 Category: Biochemistry Authors: Damjanovic L, Wilkinson H, Lloyd J Tags: Chem Senses Source Type: research

Molecular symmetry-constrained systematic search approach to structure solution of the coiled-coil SRGAP2 F-BARx domain
SRGAP2 (Slit – Robo GTPase-activating protein 2) is a cytoplasmic protein found to be involved in neuronal branching, restriction of neuronal migration and restriction of the length and density of dendritic postsynaptic spines. The extended F-BAR (F-BARx) domain of SRGAP2 generates membrane protrusions when expressed in COS-7 cells, while most F-BARs induce the opposite effect: membrane invaginations. As a first step to understand this discrepancy, the F-BARx domain of SRGAP2 was isolated and crystallized after co-expression with the carboxy domains of the protein. Diffraction data were collected from two significantly n...
Source: Acta Crystallographica Section D - November 28, 2016 Category: Biochemistry Authors: Sporny, M. Guez-Haddad, J. Waterman, D.G. Isupov, M.N. Opatowsky, Y. Tags: exhaustive search SRGAP2 F-BAR coiled coil molecular replacement research papers Source Type: research

Comparative database search engine analysis on massive tandem mass spectra of pork-based food products for halal proteomics
This study highlights the use of different database search engines (Comet, X! Tandem, ProteinProspector, and ProteinPilot™) and their respective algorithms to analyse 135 raw tandem mass spectrometry data files from 15 types of pork-based food products. This is the first attempt that has compared different database search engines in the context of halal proteomics to ensure the effectiveness of controlling the FDR. Previous studies were just focused on the advantages of a certain algorithm over another. Moreover, other previous studies also have mainly reported the use of mass spectrometry-based shotgun proteomics for me...
Source: Journal of Proteomics - April 24, 2021 Category: Biochemistry Authors: Siti Hajar Amir Mohd Hafis Yuswan Wan Mohd Aizat Muhammad Kamaruzaman Mansor Mohd Nasir Mohd Desa Yus Aniza Yusof Lai Kok Song Shuhaimi Mustafa Source Type: research

AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results
J Proteomics. 2021 Aug 10:104350. doi: 10.1016/j.jprot.2021.104350. Online ahead of print.ABSTRACTCharacterization of post-translational modifications is among the most challenging tasks in tandem mass spectrometry-based proteomics which has yet to find an efficient solution. The ultra-tolerant (open) database search attempts to meet this challenge. However, interpretation of the mass shifts observed in open search still requires an effective and automated solution. We have previously introduced the AA_stat tool for analysis of amino acid frequencies at different mass shifts and generation of hypotheses on unaccounted in v...
Source: Journal of Proteomics - August 14, 2021 Category: Biochemistry Authors: Lev I Levitsky Julia A Bubis Mikhail V Gorshkov Irina A Tarasova Source Type: research

ReCom: A semi-supervised approach to ultra-tolerant database search for improved identification of modified peptides
We present a proof-of-concept study using Comet-ReCom, an improved version of Comet-PTM. Comet-ReCom increased identification performance of Comet-PTM by 68%. This increased performance of Comet-ReCom to score the MS/MS spectrum comes in parallel with a significantly better assignation of the monoisotopic peak of the precursor peptide in the MS spectrum, even in cases of peptide coelution. Our data demonstrate that open searches using ultra-tolerant mass windows can benefit from using a semi-supervised approach that takes advantage from previous knowledge on the nature of protein modifications. SIGNIFICANCE: The present st...
Source: Journal of Proteomics - July 18, 2023 Category: Biochemistry Authors: Andrea Laguillo-G ómez Enrique Calvo Noa Mart ín-Cófreces Marta Lozano-Prieto Francisco S ánchez-Madrid Jes ús Vázquez Source Type: research

HisPhosSite: A comprehensive database of histidine phosphorylated proteins and sites
J Proteomics. 2021 May 10:104262. doi: 10.1016/j.jprot.2021.104262. Online ahead of print.ABSTRACTHistidine phosphorylation is critically important in a variety of cellular processes including signal transduction, cell cycle, proliferation, differentiation, and apoptosis. It is estimated to account for 6% of all phosphorylated amino acids. However, due to the acid lability of the PN bond, the study of pHis lags far behind that of pSer, pThr, and pTyr. Recently, the development and use of pHis-specific antibodies and methodologies have led to a resurgence in the study of histidine phosphorylation. Although a considerable nu...
Source: Journal of Proteomics - May 13, 2021 Category: Biochemistry Authors: Jian Zhao Lingxiao Zou Yan Li Xiaofei Liu Cong Zeng Chen Xu Bin Jiang Xuejiang Guo Xiaofeng Song Source Type: research

The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes
Biochem Soc Trans. 2021 May 18:BST20200709. doi: 10.1042/BST20200709. Online ahead of print.ABSTRACTTranscription factors (TFs) regulate transcription of their target genes by identifying and binding to regulatory regions of the genome among billions of potential non-specific decoy sites, a task that is often presented as a 'needle in the haystack' challenge. The TF search process is now well understood in bacteria, but its characterization in eukaryotes needs to account for the complex organization of the nuclear environment. Here we review how live-cell single molecule tracking is starting to shed light on the TF search ...
Source: Biochemical Society Transactions - May 18, 2021 Category: Biochemistry Authors: Matteo Mazzocca Tom Fillot Alessia Loffreda Daniela Gnani Davide Mazza Source Type: research

Algorithms for Database-Dependent Search of MS/MS Data
The frequent used bottom-up strategy for identification of proteins and their associated modifications generate nowadays typically thousands of MS/MS spectra that normally are matched automatically against a protein sequence database. Search engines that take as input MS/MS spectra and a protein sequence database are referred as database-dependent search engines. Many programs both commercial and freely available exist for database-dependent search of MS/MS spectra and most of the programs have excellent user documentation. The aim here is therefore to outline the algorithm strategy behind different search engines rather t...
Source: Springer protocols feed by Protein Science - May 16, 2013 Category: Biochemistry Source Type: news

Detection and verification of 2.3 million cancer mutations in NCI60 cancer cell lines with a cloud search engine.
We present and examine the abilities of Bolt, a new cloud-based proteomics search engine to search for the presence of over 2.3 million known cancer mutations in a matter of minutes while still performing a standard proteomics search that includes 31 post translational modifications. We use previously published proteomics data sets and identify mutations that are verified using genomic studies as well as previous proteomics efforts. Our results also emphasize the need to search for mutations in a comprehensive manner while still searching for both common and rare PTMs. SIGNIFICANCE: We present and examine the abilities of ...
Source: Journal of Proteomics - August 20, 2019 Category: Biochemistry Authors: Prakash A, Majumder S, Ahmad S, Varkey M, Anish TA, Jenkins C, Rigby M, Orsburn B Tags: J Proteomics Source Type: research

Large Precursor Tolerance Database Search - A Simple Approach for Estimation of the Amount of Spectra with Precursor Mass Shifts in Proteomic Data.
Abstract Mass measurement and precursor mass assignment are independent processes in proteomic data acquisition. Due to misassignments to C-13 peak, or for other reasons, extensive precursor mass shifts (i.e., deviations of the measured from calculated precursor neutral masses) in LC-MS/MS data obtained with the high-accuracy LTQ-Orbitrap mass spectrometers have been reported in previous studies. Although computational methods for post-acquisition reassignment to monoisotopic mass have been developed to curate the MS/MS spectra prior to database search, a simpler method for estimating the fraction of spectra with ...
Source: Journal of Proteomics - August 7, 2013 Category: Biochemistry Authors: Weng RR, Chu LJ, Shu HW, Wu TH, Chen MC, Chang Y, Tsai YS, Wilson MC, Tsay YG, Goodlett DR, Ng WV Tags: J Proteomics Source Type: research