Abstract:
:Aberrant protein phosphorylation plays important roles in cancer-related cell signaling. With the goal of achieving multiplexed, comprehensive, and fully automated relative quantitation of site-specific phosphorylation, we present a simple label-free strategy combining an automated pH/acid-controlled IMAC procedure and informatics-assisted SEMI (sequence, elution time, mass-to-charge, and internal standard) algorithm. The SEMI strategy effectively increased the number of quantifiable peptides more than 4-fold in replicate experiments (from 262 to 1171, p < 0.05, false discovery rate = 0.46%) by using a fragmental regression algorithm for elution time alignment followed by peptide cross-assignment in all LC-MS/MS runs. In addition, the strategy demonstrated good quantitation accuracy (10-12%) for standard phosphoprotein and variation less than 1.9 fold (within 99% confidence range) in proteome scale and reliable linear quantitation correlation (R(2) = 0.99) with 4000-fold dynamic concentrations, which was attributed to our reproducible experimental procedure and informatics-assisted peptide alignment tool to minimize system variations. In an attempt to explore metastasis-associated phosphoproteomic alterations in lung cancer, this approach was used to delineate differential phosphoproteomic profiles of a lung cancer metastasis model. Without sample fractionation, the SEMI algorithm enabled quantification of 1796 unique phosphopeptides (false discovery rate = 0.56%) corresponding to 854 phosphoproteins from a series of non-small cell lung cancer lines with varying degrees of in vivo invasiveness. Nearly 40% of the phosphopeptides showed >2-fold change in highly invasive cells; validation of phosphoprotein subsets by Western blotting not only demonstrated the consistency of data obtained by our SEMI strategy but also revealed that such dramatic changes in the phosphoproteome result mostly from translational or post-translational regulation. Mapping of these differentially expressed phosphoproteins in multiple cellular pathways related to cancer invasion and metastasis suggests that the site and degree of phosphorylation might have distinct patterns or functions in the complex process of cancer progression.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Wang YT,Tsai CF,Hong TC,Tsou CC,Lin PY,Pan SH,Hong TM,Yang PC,Sung TY,Hsu WL,Chen YJdoi
10.1021/pr100394usubject
Has Abstractpub_date
2010-11-05 00:00:00pages
5582-97issue
11eissn
1535-3893issn
1535-3907journal_volume
9pub_type
杂志文章abstract::Bacterial small RNAs (sRNAs) and two-component systems (TCSs) were two vital regulatory mechanisms employed by microorganisms to respond to environmental changes and stresses. As a promising "autotrophic cell factory", photosynthetic cyanobacteria have attracted a lot of attention these years. Although most studies fo...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00243
更新日期:2017-08-04 00:00:00
abstract::The protein kinase AKT is a central kinase in the heart and has a major impact on growth/hypertrophy, survival/apoptosis, and metabolism. To gain more insight into AKT isoform-specific signaling at the molecular level, we investigated the phosphoproteome of HL-1 cardiomyocytes carrying AKT1 or AKT2 isoform-specific kn...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500131g
更新日期:2014-10-03 00:00:00
abstract::The past decade has been marked by the emergence of selective affinity media and sensitive mass spectrometry instrumentation that facilitated large-scale phosphoproteome analyses and expanded the repertoire of protein phosphorylation. Despite these remarkable advances, the precise location of the phosphorylation site ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr300229m
更新日期:2012-07-06 00:00:00
abstract::Quantitative comparison of protein expression levels in 2D gels is complicated by the variables associated with protein separation and mass spectrometric responses. Metabolic labeling allows cells from different experiments to be mixed prior to analysis. This approach has been reported for prokaryotic cells. Here, we ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr025523f
更新日期:2002-07-01 00:00:00
abstract::Linear, short-chain polyfluorinated and perfluorinated alkyl compounds, often referred to as PFCs, have been in worldwide use as surfactants and polymer precursors for decades, and environmental dispersal of these highly persistent compounds represents a public health threat. Whereas ubiquitous low-level exposure to t...
journal_title:Journal of proteome research
pub_type: 杂志文章,评审
doi:10.1021/pr500990w
更新日期:2015-01-02 00:00:00
abstract::Tumor invasion defines the transition between tissue-restricted carcinomas, related to good outcome as optimal surgery becomes possible, and metastatic tumors associated with poor prognosis and a dramatic decrease in survival. In endometrial cancer, myometrial infiltration represents a determinant parameter highly val...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr900390t
更新日期:2009-10-01 00:00:00
abstract::There are new challenges for hazard and risk assessment in the chemical industry with regard to REACH legislation in Europe and related activities in the U.S. and Japan, which require the development of novel in vitro models for the molecular characterization of drug- or chemical-related effects replacing conventional...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr100514e
更新日期:2010-11-05 00:00:00
abstract::Connective tissues such as tendon, ligament and cartilage are mostly composed of extracellular matrix (ECM). These tissues are insoluble, mainly due to the highly cross-linked ECM proteins such as collagens. Difficulties obtaining suitable samples for mass spectrometric analysis render the application of modern proteo...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00806
更新日期:2016-12-02 00:00:00
abstract::A major challenge in the life sciences is the extraction of detailed molecular information from plants and animals that are not among the handful of exhaustively studied "model organisms." As a consequence, certain species with novel phenotypes are often ignored due to the lack of searchable databases, tractable genet...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr050306a
更新日期:2006-04-01 00:00:00
abstract::Birth weight is an important indicator of maternal and fetal health and a predictor of health in later life. However, the determinants of variance in birth weight are still poorly understood. We aimed to identify the biological pathways, which may be perturbed by environmental exposures, that are important in determin...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00846
更新日期:2018-03-02 00:00:00
abstract::Phosphorylation is a post-translational modification with a vital role in cellular signaling. Isobaric labeling-based strategies, such as tandem mass tags (TMT), can measure the relative phosphorylation states of peptides in a multiplexed format. However, the low stoichiometry of protein phosphorylation constrains the...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00759
更新日期:2020-01-03 00:00:00
abstract::Eusocial behavior is extensively studied in the honeybee, Apis mellifera, as it displays an extreme form of altruism. Honeybee workers are generally obligatory sterile in a bee colony headed by a queen, but the inhibition of ovary activation is lifted upon the absence of queen and larvae. Worker bees are then able to ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr201222s
更新日期:2012-05-04 00:00:00
abstract::The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.7b00445
更新日期:2017-09-01 00:00:00
abstract::Microorganisms release effector molecules that modulate the host machinery enabling survival, replication, and dissemination of a pathogen. Here we characterized the extracellular proteome of Paracoccidioides brasiliensis at its pathogenic yeast phase. Cell-free culture supernatants from the Pb18 isolate, cultivated i...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr200872s
更新日期:2012-03-02 00:00:00
abstract::While the proteome defines the expressed gene products, the metabolome results from reactions controlled by such gene products. Plasma represents an accessible "window" to the metabolome both in regard of availability and content. The wide range of the plasma metabolome, in terms of molecular diversity and abundance, ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr8001639
更新日期:2008-08-01 00:00:00
abstract::We compared the metabolomic profile of aqueous humor from patients with primary open-angle glaucoma (POAG; n = 26) with that of a group of age- and sex-matched non-POAG controls (n = 26), all participants undergoing cataract surgery. Supervised paired partial least-squares discriminant analysis showed good predictive ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00915
更新日期:2019-03-01 00:00:00
abstract::Although the "missing protein" is a temporary concept in C-HPP, the biological information for their "missing" could be an important clue in evolutionary studies. Here we classified missing-protein-encoding genes into two groups, the genes encoding PE2 proteins (with transcript evidence) and the genes encoding PE3/4 p...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.5b00450
更新日期:2015-12-04 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
abstract::De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight gr...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4008078
更新日期:2014-02-07 00:00:00
abstract::A major challenge in developing cell therapies is reliable characterization of the cell product at the molecular level. Fresh autologous and passaged human bone marrow enriched for stem and mesenchymal stromal stem cells have been used to regenerate bone. We report the proteome of an innovative autologous human bone m...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr801064u
更新日期:2009-04-01 00:00:00
abstract::Increased throughput as well as increased multiplexing of liquid chromatography coupled to selected reaction monitoring mass spectrometry (LC-SRM-MS) assays for protein quantification challenges routine data analysis. Despite the measurement of multiple transitions from multiple peptides, for clinical applications a s...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.9b00854
更新日期:2020-06-05 00:00:00
abstract::Ovarian granulosa cell tumors (GCTs) are hormonally active cancers characterized by indolent growth and late, invasive relapse. No therapies have yet proven to be efficacious. We previously reported that the inhibition of the antiapoptotic X-linked inhibitor of apoptosis protein (XIAP) removes transrepression of the p...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.8b00917
更新日期:2019-04-05 00:00:00
abstract::Method development is one of the objectives of the astrophysical community for characterizing the organic matter in objects of the solar system. In this context, we report on the development of an enzyme-catalyzed stereoselective hydrolysis, inspired by the proteomics discipline, which has enabled the indirect detecti...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.0c00700
更新日期:2020-10-20 00:00:00
abstract::The skin is the primary boundary between the body and the environment. In addition to its properties as a physical barrier, skin keratinocytes actively participate in many defense mechanisms. Viral double-stranded RNA (dsRNA) is the most important viral structure involved in activation of immune response. Intracellula...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr901040u
更新日期:2010-03-05 00:00:00
abstract::Preeclampsia is a pregnancy-specific hypertensive syndrome and a major cause of maternal and fetal morbidity and mortality. At the present time, no reliable screening tests to identify women at risk are available. We have compared the amniotic fluids (AF) proteomic maps of five preeclamptic patients with those of five...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr060315z
更新日期:2007-01-01 00:00:00
abstract::The notion of a gamete recognition system that alerts females to the presence of gametes in their reproductive tract profoundly influences our understanding of the physiology of events leading to conception and the bearing of offspring. Here, we show that the female responds to gametes within her tract by modulating t...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr070349m
更新日期:2007-12-01 00:00:00
abstract::Visual signal transduction takes place on the surface of flat membrane vesicles called photoreceptor discs, which reside inside the light-sensitive outer segment organelle of vertebrate photoreceptor cells. Although biochemical studies have indicated that discs are built with a handful of highly specialized proteins, ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr4003678
更新日期:2013-06-07 00:00:00
abstract::The development of chronic heart failure (CHF) following myocardial infarction is characterized by progressive alterations of left ventricle (LV) structure and function called left ventricular remodeling (LVR), but the mechanism of LVR remains still unclear. Moreover, information concerning the global alteration prote...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr800409u
更新日期:2008-11-01 00:00:00
abstract::Many neurodegenerative diseases, such as Parkinson's disease, can be directly correlated with the deregulation in neuronal signaling. Hence, it is indispensable for therapy development to understand the participating signaling processes. Because the activity of the involved protein kinases is of major interest for the...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/pr500163r
更新日期:2014-08-01 00:00:00
abstract::Clematis terniflora DC. has potential pharmaceutical value; on the contrary, high-level UV-B irradiation with dark treatment led to the accumulation of secondary metabolites. Metabolomic and proteomic analyses of leaf of C. terniflora were performed to investigate the systematic response mechanisms to high-level UV-B ...
journal_title:Journal of proteome research
pub_type: 杂志文章
doi:10.1021/acs.jproteome.6b00206
更新日期:2016-08-05 00:00:00