Abstract：
:Quantitative proteomic comparisons require a sufficient number of samples to reach an acceptable level of significance. But 2D gel electrophoresis commonly results in incomplete data sets due to spots with missing values reducing thereby the number of parallel measurements for individual proteins. Here we investigated how many missing values per spot can be tolerated. The number of spots in common between all gels was found to decrease with the number of parallel gels in a non-linear fashion. Increasing numbers of missing values were associated with a moderate increase in the quantitative variation of spot volumes. Based on the missing value pattern in 20 gels we performed an analysis of the multiple testing power for the hypothetical scenario of a comparative 2DE study with six or twelve parallel gels. The calculation considered the statistical power of the individual spot as well as the number of spots included in the analysis. The power increased with inclusion of spots with higher number of missing values and showed an optimum at a specific minimum number of spot replicates. The results suggest that proteins with missing values can be included in a univariate analysis as long as a sufficient number of parallel gels are made.
journal_name
J Proteomicsjournal_title
Journal of proteomicsauthors
Zellner M,Graf A,Zehetmayer S,Winkler W,Staes A,Gevaert K,Vandekerckhove J,Marchetti-Deschmann M,Miller I,Bauer P,Allmaier G,Oehler Rdoi
10.1016/j.jprot.2011.12.019subject
Has Abstractpub_date
2012-03-16 00:00:00pages
1792-802issue
6eissn
1874-3919issn
1876-7737pii
S1874-3919(11)00700-7journal_volume
75pub_type
杂志文章abstract：:One of the main concerns about genetically modified foods and their potential impacts on human health is that the introduction of a new/ altered gene may putatively alter the expression of others, namely endogenous allergens. We intended to evaluate, and to compare, using quantitative real time RT-PCR technique, the e...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.01.005
更新日期：2012-04-03 00:00:00
abstract：:Much attention has been paid to the broodiness of the Muscovy duck, but the molecular mechanism of broodiness remains largely unknown. In this study, the ovary tissues of Muscovy ducks during the broody and laying periods were used to investigate differentially expressed proteins (DEPs) by the iTRAQ-based proteomics a...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103401
更新日期：2019-07-30 00:00:00
abstract：UNLABELLED:The long cultivation of field pea led to an enormous diversity which, however, seems to hold just little resistance against the ascochyta blight disease complex. The potential of below ground microbial symbiosis to prime the immune system of Pisum for an upcoming pathogen attack has hitherto received little ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.03.018
更新日期：2016-06-30 00:00:00
abstract：:Combinatorial peptide ligand libraries (CPLLs) have been adopted for harvesting and identifying traces of casein (used as a fining agent) present in white wines. Although minute amounts (200 microL) of CPLL beads are added to the entire content of a wine bottle (750 mL), they are able to sequester with high efficiency...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2010.05.010
更新日期：2010-08-05 00:00:00
abstract：UNLABELLED:Isotopic labeling and isobaric labeling are two kinds of the typical quantification method that have been widely used in proteomics analysis. Herein, a novel quantitative strategy, partially isobaric peptide termini labeling (PITL), was developed to overcome the drawbacks of each above-mentioned labeling str...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.11.014
更新日期：2015-01-30 00:00:00
abstract：:Several proteomics studies have been conducted to identify new cerebrospinal fluid (CSF) biomarkers in Multiple Sclerosis (MuS). However, the complexity of CSF and its invasive collection, limits its use. Therefore, the goal of biomarker research in MuS is to identify novel distinctive targets in CSF or in easily acce...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103403
更新日期：2019-07-30 00:00:00
abstract：:The aim of the present study was to evaluate the differences in salivary proteome at rest and in response to an acute exercise in men and women. For this, unstimulated whole saliva samples in rest and after a bout resistance exercise leading to failure (ELF) of both men and women (n = 5 for each sex) were subjected to...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103629
更新日期：2020-03-01 00:00:00
abstract：:Populations of small eukaryotic RNAs, in addition to relatively well recognized molecules such as miRNAs or siRNAs, also contain fragments derived from all classes of constitutively expressed non-coding RNAs. It has been recently demonstrated that the formation and accumulation of RNA fragments (RFs) is cell-/tissue-s...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.10.007
更新日期：2019-02-20 00:00:00
abstract：UNLABELLED:Mapping protein-protein interactions for chromatin-associated proteins remains challenging. Here we explore the use of BioID, a proximity biotinylation approach in which a mutated biotin ligase (BirA*) is fused to a bait of interest, allowing for the local activation of biotin and subsequent biotinylation of...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.09.011
更新日期：2015-04-06 00:00:00
abstract：:Early response to 7 days of prednisolone (PRED) treatment is one of the important prognostic factors in predicting eventual outcome in childhood acute lymphoblastic leukemia (ALL). Using proteomic tools and clinically important leukemia cell lines (REH, 697, Sup-B15, RS4; 11), we have identified potential prognostic p...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.02.034
更新日期：2011-05-16 00:00:00
abstract：UNLABELLED:Clostridium difficile spores are considered the morphotype of infection, transmission and persistence of C. difficile infections. There is a lack of information on the composition of the outermost exosporium layer of C. difficile spores. Using recently developed exosporium removal methods combined with MS/MS...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.03.035
更新日期：2015-06-18 00:00:00
abstract：UNLABELLED:The aim of this study was to search for immunogenic schistosomula proteins in the hope of identifying novel intervention targets. Schistosomula proteins were analyzed by immunoproteomic which the probes were sera derived from BALB/c mice (susceptible hosts) and Microtus fortis (resistant hosts). A total of 1...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.04.010
更新日期：2015-06-21 00:00:00
abstract：:Searching for potential predictors of meat color is a challenging task for the meat industry. In this study, the relationship between meat color parameters and the sarcoplasmic proteome of M. longissimuss lumborum (LL) and M. psoas major (PM) from Chinese Luxi yellow cattle during post-mortem storage (0, 5, 10 and 15d...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.10.027
更新日期：2016-09-16 00:00:00
abstract：:Protein methylation is one of the common post-translational modifications involved in diverse biological processes including signal transduction, transcriptional regulation, DNA repairing, gene activation, gene repression, and RNA processing. Due to technique limitation, the investigation of protein methylation in can...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103738
更新日期：2020-05-15 00:00:00
abstract：:Mass spectrometry imaging (MSI) enables the direct analysis of molecules from the surface of a wide variety of samples, allowing the multiplex measurement of both abundance and distribution of small molecules, lipids, peptides and proteins. As the technology has been refined an increasing number of ionization methods ...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2012.04.012
更新日期：2012-08-30 00:00:00
abstract：:Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the leve...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.05.010
更新日期：2019-01-16 00:00:00
abstract：:MALDI Mass Spectrometry Imaging has shown important potential for molecular classification and pathology marker discovery. Protein markers identification is therefore of prime importance. Direct structural analysis from tissue sections has shown limitations for protein identification because of the high degree of comp...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.11.025
更新日期：2013-02-21 00:00:00
abstract：UNLABELLED:Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.09.012
更新日期：2013-12-06 00:00:00
abstract：:Organic farming aims to be environmentally sound, but the question as to whether organic cropping brings more nutritional benefits to farmers and consumers than the conventional cropping needs still to be answered. To gain insights into the molecular effects of organic farming we used proteome analysis to analyze cabb...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.06.021
更新日期：2011-11-18 00:00:00
abstract：UNLABELLED:Sympatric distribution and sharing of hosts and antigens by Trypanosoma rangeli and Trypanosoma cruzi, the etiological agent of Chagas' disease, often incur in misdiagnosis and improper epidemiological inferences. Many secreted and surface proteins (SP) have been described as important antigens shared by the...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.02.011
更新日期：2013-04-26 00:00:00
abstract：UNLABELLED:The membrane-associated LonB protease is essential for viability in Haloferax volcanii, however, the cellular processes affected by this protease in archaea are unknown. In this study, the impact of a lon conditional mutation (down-regulation) on H. volcanii physiology was examined by comparing proteomes of ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.03.016
更新日期：2015-05-21 00:00:00
abstract：:We carried out a comparative proteomic study to explore the molecular mechanisms that underlie the defense response of Douglas-fir (DF, Pseudotsuga menziesii) to laminated root rot, a disease caused by Phellinus sulphurascens. 2-DE was conducted on proteins extracted from roots of laboratory-grown, young DF seedlings ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2008.06.004
更新日期：2008-10-07 00:00:00
abstract：:High-throughput technologies were used to identify venom gland toxin expression and to characterize the venom proteomes of two rear-fanged snakes, Ahaetulla prasina (Asian Green Vine Snake) and Borikenophis portoricensis (Puerto Rican Racer). Sixty-nine complete toxin-coding transcripts from 12 venom protein superfami...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.08.004
更新日期：2018-09-15 00:00:00
abstract：UNLABELLED:Erwinia amylovora is a Gram-negative plant pathogen that causes fire blight. This disease affects most members of the Rosaceae family including apple and pear. Here, an infection model is introduced to study proteomic changes in a highly virulent E. amylovora strain upon interaction with its host as compared...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.02.018
更新日期：2016-04-29 00:00:00
abstract：:This review is the continuation of three previously published articles [Jorrin JV, Maldonado AM, Castillejo MA. Plant proteome analysis: a 2006 update. Proteomics 2007; 7: 2947-2962; Rossignol M, Peltier JB, Mock HP, Matros A, Maldonado AM, Jorrin JV. Plant proteome analysis: a 2004-2006 update. Proteomics 2006; 6: 55...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2009.01.026
更新日期：2009-04-13 00:00:00
abstract：:Posttranslational modification by ubiquitination targets proteins for degradation, recycling, stabilization or altered trafficking, and as such can alter cellular signaling pathways. The substrate specificity of this multistep process is controlled by ubiquitin ligases, including those of the HECT domain-containing NE...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103830
更新日期：2020-07-15 00:00:00
abstract：UNLABELLED:The mechanisms underlying resistance to challenge by gastrointestinal nematode parasites in sheep are complex. Using DIGE, we profiled ovine lymph proteins in lambs with host resistance (R), resilience (Ri) or susceptibility (S) to a daily trickle challenge with the nematode Trichostrongylus colubriformis. E...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.07.017
更新日期：2014-09-23 00:00:00
abstract：:The effect of nitrogen on Fusarium Head Blight (FHB) in a susceptible barley cultivar was investigated using gel-based proteomics. Barley grown with either 15 or 100kgha(-1)N fertilizer was inoculated with Fusarium graminearum (Fg). The storage protein fraction did not change significantly in response either to N leve...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2009.10.010
更新日期：2010-02-10 00:00:00
abstract：:Flightin is a myosin binding phosphoprotein that originated in the ancestor to Pancrustacea ~500 MYA. In Drosophila melanogaster, flightin is essential for length determination and flexural rigidity of thick filaments. Here, we show that among 12 Drosophila species, the N-terminal region is characterized by low sequen...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.12.006
更新日期：2016-03-01 00:00:00
abstract：:In the development of ischemia/reperfusion (I/R) injury, the role of the myosin light chain (MLC) phosphorylation has been given increased consideration. ML-7, a MLC kinase inhibitor, has been shown to protect cardiac function from I/R, however the exact mechanism remains unclear. Isolated rat hearts were perfused und...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.06.016
更新日期：2012-09-18 00:00:00
