Abstract:
:Mass spectrometry is being used to identify protein biomarkers that can facilitate development of drug treatment. Mass spectrometry-based labeling proteomic experiments result in complex proteomic data that is hierarchical in nature often with small sample size studies. The generalized linear model (GLM) is the most popular approach in proteomics to compare protein abundances between groups. However, GLM does not address all the complexities of proteomics data such as repeated measures and variance heterogeneity. Linear models for microarray data (LIMMA) and mixed models are two approaches that can address some of these data complexities to provide better statistical estimates. We compared these three statistical models (GLM, LIMMA, and mixed models) under two different normalization approaches (quantile normalization and median sweeping) to demonstrate when each approach is the best for tagged proteins. We evaluated these methods using a spiked-in data set of known protein abundances, a systemic lupus erythematosus (SLE) data set, and simulated data from multiplexed labeling experiments that use tandem mass tags (TMT). Data are available via ProteomeXchange with identifier PXD005486. We found median sweeping to be a preferred approach of data normalization, and with this normalization approach there was overlap with findings across all methods with GLM being a subset of mixed models. The conclusion is that the mixed model had the best type I error with median sweeping, whereas LIMMA had the better overall statistical properties regardless of normalization approaches.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
D'Angelo G,Chaerkady R,Yu W,Hizal DB,Hess S,Zhao W,Lekstrom K,Guo X,White WI,Roskos L,Bowen MA,Yang Hdoi
10.1021/acs.jproteome.6b01050subject
Has Abstractpub_date
2017-09-01 00:00:00pages
3124-3136issue
9eissn
1535-3893issn
1535-3907journal_volume
16pub_type
杂志文章abstract::Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic methods have been widely used to identify lysine acylation proteins. However, these experimental approaches often fail to detect proteins that are in low abundance or absent in specific biological samples. To circumvent these problems, we develo...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00240
更新日期:2016-12-02 00:00:00
abstract::Ozonated autohemotherapy (O3-AHT) is a medical approach during which blood obtained from the patient is ozonated and injected back into the body. Despite an increasing number of evidence that O3-AHT is safe, this type of therapy remains controversial. To extend knowledge about the changes in blood evoked by O3-AHT, LC...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr3008946
更新日期:2012-12-07 00:00:00
abstract::Due to their ease of use and high binding affinity, streptavidin-based purification tools have become widely used for isolating biotinylated compounds from complex mixtures. We and others routinely use streptavidin-sepharose matrices to isolate biotinylated polypeptides generated in proximity-dependent biotinylation a...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.0c00117
更新日期:2020-08-07 00:00:00
abstract::The role played by the degree of folding of protein backbones in explaining the binding energetics of protein-ligand interactions has been studied. We analyzed the protein/peptide interactions in the RNase-S system in which amino acids at two positions of the peptide S have been mutated. The global degree of folding o...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr0503174
更新日期:2006-01-01 00:00:00
abstract::The International Mouse Phenotyping Consortium program has been established to ascribe biological functions to systematically knocked-out (KO) genes by in vivo and ex vivo phenotyping. The plasma clinical chemistry screen includes an assessment of liver, kidney, and bone function and provides a basic lipid profile and...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr501039k
更新日期:2015-05-01 00:00:00
abstract::The majority of mitochondrial preproteins are targeted via N-terminal presequences that are cleaved upon import into the organelle. The essential mitochondrial processing protease (MPP) is assumed to cleave the majority of incoming precursors; however, only a small fraction of mitochondrial precursors have been experi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00327
更新日期:2015-11-06 00:00:00
abstract::We report here using a novel technology-electrospray-assisted laser desorption ionization (ELDI)/mass spectrometry-for the rapid and sensitive detection of the major proteins that exist in dried biological fluids (e.g., blood, tears, saliva, serum), bacterial cultures, and tissues (e.g., porcine liver and heart) under...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr050442f
更新日期:2006-05-01 00:00:00
abstract::The phagosome is very important to host immunity and tissue homeostasis maintenance. The destiny of the phagosome is closely associated with the outcome of the pathogen within. Most pathogens are successfully delivered to the lysosome and destroyed via the fusion of the phagosome with the lysosome. Mycobacterium tube...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/pr300125t
更新日期:2012-05-04 00:00:00
abstract::Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in eight cases of BAL fluid, as well as eight lung adenocarcinoma tissues ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400274w
更新日期:2013-08-02 00:00:00
abstract::Sterols are membrane-bound isoprenoid lipids that are required for cell viability and growth. In plants, it is generally assumed that 3-hydroxy-3-methylglutaryl-CoA-reductase (HMGR) is a key element of their biosynthesis, but the molecular regulation of that pathway is largely unknown. In an attempt to identify regula...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr201127u
更新日期:2012-02-03 00:00:00
abstract::Cystinuria is a purely renal, rare genetic disease caused by mutations in cystine transporter genes and characterized by defective cystine reabsorption leading to kidney stones. In 14% of cases, patients undergo nephrectomy, but given the difficulty to predict the evolution of the disease, the identification of marker...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr501003q
更新日期:2015-01-02 00:00:00
abstract::In systemic amyloidosis, accumulation of misfolded proteins as extracellular amyloid fibrils in tissues causes severe organ dysfunction, but the molecular events of tissue damage related to amyloid deposition are still largely unknown. Through the use of the MudPIT proteomic approach, comprehensive protein profiles of...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr400583h
更新日期:2013-12-06 00:00:00
abstract::The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked wit...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00370
更新日期:2017-12-01 00:00:00
abstract::Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g., with affi...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00927
更新日期:2019-05-03 00:00:00
abstract::Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. H...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500196b
更新日期:2014-12-05 00:00:00
abstract::New mass-tagging reagents for quantitative proteomics measurements have been designed using solid phase peptide synthesis technology. The solid phase mass tags have been used to accurately measure the relative amounts of cysteine-containing peptides in model peptide mixtures as well as in mixtures of tryptic digests i...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr034081k
更新日期:2004-01-01 00:00:00
abstract::Although tandem mass spectrometry (MS/MS) has become an integral part of proteomics, intensity patterns in MS/MS spectra are rarely weighted heavily in most widely used algorithms because they are not yet fully understood. Here a knowledge mining approach is demonstrated to discover fragmentation intensity patterns an...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070106u
更新日期:2008-01-01 00:00:00
abstract::Protein-protein control recognition remains a huge challenge, and its development depends on understanding the chemical and biological mechanisms by which these interactions occur. Here we describe a protein-protein control recognition technique based on the dominant electrostatic interactions occurring between the pr...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100027k
更新日期:2010-06-04 00:00:00
abstract::Snake venoms are biological weapon systems composed of secreted proteins and peptides that are used for immobilizing or killing prey. Although post-translational modifications are widely investigated because of their importance in many biological phenomena, we currently still have little understanding of how protein g...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00217
更新日期:2016-08-05 00:00:00
abstract::Fusarium graminearum (FG) is a serious plant pathogen causing huge losses in global production of wheat and other cereals. Tri5-gene encoded trichodiene synthase is the first key enzyme for biosynthesis of trichothecene mycotoxins in FG. To further our understandings of FG metabolism which is essential for developing ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr101095t
更新日期:2011-05-06 00:00:00
abstract::Protein lysine acylation, including acetylation and succinylation, has been found to be a major post-translational modification (PTM) and is associated with the regulation of cellular processes that are widespread in bacteria. Vibrio parahemolyticus is a model marine bacterium that causes seafood-borne illness in huma...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00485
更新日期:2015-10-02 00:00:00
abstract::An efficient means for the identification of prognostic and predictive biomarkers is essential in today's cancer management. A new approach toward biomarker discovery has therefore been proposed, where pathways instead of individual proteins would be monitored and targeted. Recently, the 'secretome', a biological flui...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr8008572
更新日期:2009-03-01 00:00:00
abstract::The Human Proteome Project (HPP) has made great efforts to clarify the existing evidence of human proteins since 2012. However, according to the recent release of neXtProt (2019-1), approximately 10% of all human genes still have inadequate or no experimental evidence of their translation at the protein level. They we...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00355
更新日期:2019-12-06 00:00:00
abstract::Energy imbalance is a primary cause of obesity. While the classical approach to attenuate weight gain includes an increase in energy expenditure through exercise, dietary manipulation such as the inclusion of dairy products has also been proven effective. In the present study, we explored the potential mechanisms by w...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00304
更新日期:2019-11-01 00:00:00
abstract::Ovarian cancer remains a deadly threat to women as the disease is often diagnosed in the late stages when the chance of survival is low. There are no good biomarkers available for early detection and only a few markers have shown clinical utility for prognosis, response to therapy and disease recurrence. We mined cond...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900411g
更新日期:2009-10-01 00:00:00
abstract::O-Linked N-acetyl-β-d-glucosamine (O-GlcNAc) is a dynamic post-translational modification that modifies and regulates over 3000 nuclear, cytoplasmic, and mitochondrial proteins. Upon exposure to stress and injury, cells and tissues increase the O-GlcNAc modification, or O-GlcNAcylation, of numerous proteins promoting ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00369
更新日期:2016-12-02 00:00:00
abstract::After tissue or body fluid sampling, proteases and other protein-modifying enzymes can rapidly change composition of the proteome. As a direct consequence, analytical results will reflect a mix of in vivo proteome and ex vivo degradation products. Vital information about the presampling state may be destroyed or disto...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr8006446
更新日期:2009-02-01 00:00:00
abstract::Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900365e
更新日期:2009-10-01 00:00:00
abstract::Endometrial cancer (EC) is the most frequent gynecological cancer. Tumor dissemination affecting ∼20% of EC patients is characterized at the primary carcinoma by epithelial-to-mesenchymal transition (EMT) associated with myometrial infiltration. At distant sites, the interaction of circulating tumor cells (CTCs) with ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00750
更新日期:2019-03-01 00:00:00
abstract::In this study we selected three breast cancer cell lines (SKBR3, SUM149 and SUM190) with different oncogene expression levels involved in ERBB2 and EGFR signaling pathways as a model system for the evaluation of selective integration of subsets of transcriptomic and proteomic data. We assessed the oncogene status with...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4001527
更新日期:2013-06-07 00:00:00