Abstract:
:In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in particular associated with the use of data-independent acquisition, it is time to perform an overview of this growing field with special focus on one of the most promising approaches: SWATH-MS, and to present future perspectives for its application as a translational tool. Therefore, a summary of this technique is presented focusing on two key relevant concepts associated with its application in biomarker discovery: the protein library and the individual digital maps concepts. It is also the purpose of this review to document the likely impact of SWATH-MS in both fundamental and translational research including biomarker identification and creation of diagnostic tools. To that end, the two concepts referred above were integrated with ongoing technical developments. Finally, some of the current restrictions for the implementation of SWATH-MS on a large scale are identified, and potential solutions presented, namely protocol standardization combined with the use of the proper standards.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Anjo SI,Santa C,Manadas Bdoi
10.1002/pmic.201600278subject
Has Abstractpub_date
2017-02-01 00:00:00issue
3-4eissn
1615-9853issn
1615-9861journal_volume
17pub_type
杂志文章,评审相关文献
PROTEOMICS文献大全abstract::The phosphorylation of heat shock protein 27 (HSP27) occurs differently in human renal cell carcinoma (RCC) compared to homologous normal kidney tissue. Two-dimensional electrophoresis was used to separate and visualize HSP27, via immunostaining with anti-HSP27 antibody, in tumor and normal renal samples, obtained aft...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401134
更新日期:2005-02-01 00:00:00
abstract::Sporozoites of the malaria parasite Plasmodium are transmitted by mosquitoes and infect the liver for an initial and obligatory round of replication, before exponential multiplication in the blood and onset of the disease. Sporozoites and liver stages provide attractive targets for malaria vaccines and prophylactic dr...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.202000305
更新日期:2021-01-16 00:00:00
abstract::In-gel peptide digestion has become a widely used technique for characterizing proteins resolved by two-dimensional gel electrophoresis. Peptides generated from gel pieces are frequently contaminated with detergent and salts. Prior to matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysi...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200202)2:2<145::aid-prot145>3.0.
更新日期:2002-02-01 00:00:00
abstract::We introduce a new methodology named ligand profiling and identification for effective discovery of bioactive ligands such as peptide hormones. This technology was developed from a new concept of parallel column chromatography and active fraction profiling by nano-LC MS. Traditional methods use sequential column chrom...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500511
更新日期:2006-03-01 00:00:00
abstract::Topoisomerase (topo) II catalyzes topological changes in DNA. Although both human isozymes, topo IIα and β are phosphorylated, site-specific phosphorylation of topo IIβ is poorly characterized. Using LC-MS/MS analysis of topo IIβ, cleaved with trypsin, Arg C or cyanogen bromide (CNBr) plus trypsin, we detected four +8...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000194
更新日期:2011-03-01 00:00:00
abstract::Mulberry dwarf (MD) is a serious infectious disease of mulberry caused by phytoplasma. Infection with MD phytoplasma results in stress phenotypes of yellowing, phyllody, stunting, proliferation, and witches' broom. Physiological and biochemical analysis has shown that infection with MD phytoplasma causes an increase i...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900012
更新日期:2009-12-01 00:00:00
abstract::Sandwich ELISA microarrays have great potential for validating disease biomarkers. Each ELISA relies on robust-affinity reagents that retain activity when immobilized on a solid surface or when labeled for detection. Single-chain antibodies (scFv) are affinity reagents that have greater potential for high-throughput p...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200701036
更新日期:2008-06-01 00:00:00
abstract::Immobilized metal affinity chromatography (IMAC) is a commonly used technique for phosphoproteome analysis due to its high affinity for adsorption of phosphopeptides. Miniaturization of IMAC column is essential for the analysis of a small amount of sample. Nanoscale IMAC column was prepared by chemical modification of...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600045
更新日期:2007-02-01 00:00:00
abstract::The HUPO Brain Proteome Project (HUPO BPP) held its 12th workshop in Toronto on 26 September 2009 prior to the HUPO VIII World Congress. The principal aim of this project is to obtain a better understanding of neurodiseases and ageing, with the ultimate objective of discovering prognostic and diagnostic biomarkers, in...
journal_title:Proteomics
pub_type:
doi:10.1002/pmic.201090042
更新日期:2010-06-01 00:00:00
abstract::Seed coat color is an important attribute determining consumption of soybean seeds. Soybean cultivar Mallikong (M) has yellow seed coat while its naturally mutated cultivar Mallikong mutant (MM), has brown colored seed coat. We used integrated proteomics and metabolomics approach to investigate the differences between...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400453
更新日期:2015-05-01 00:00:00
abstract::LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw data processing, which utilizes precursor-level high mass accuracy data for peak processing and MGF creation. In particular, ProteinPilot results from MaxQuant-processed peaklists for Orbitrap data sets resulted in improved spectral u...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100097
更新日期:2012-06-01 00:00:00
abstract::Gram-negative bacteria release outer membrane vesicles (OMVs) as part of their normal growth that contain a range of cargo from their parent bacterium, including DNA, RNA, and proteins. The protein content of OMVs is suggested to be similar in composition to various sub-cellular locations of their parent bacterium. Ho...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800209
更新日期:2019-01-01 00:00:00
abstract::Apoptosis contributes to cell death after cerebral ischaemia. A quantitative proteomics approach has been employed to define alterations in protein levels in apoptosis induced with staurosporine (STS). Human neuroblastoma derived SH-SY5Y cells were treated with STS (500 nM for 6 h) to induce apoptosis. Quantitative 2-...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600964
更新日期:2007-09-01 00:00:00
abstract::A brief period of ischemia followed by timely reperfusion may lead to prolonged, yet reversible, contractile dysfunction (myocardial stunning). Damage to the myocardium occurs not only during ischemia, but also during reperfusion, where a massive release of oxygen-free radicals (OFR) occurs. We have previously utilize...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600219
更新日期:2006-12-01 00:00:00
abstract::When the p-value is set at <0.05 in statistical group comparisons, a 5% rate of "false significant" results is expected. In order to test the reliability of our 2-DE method, we loaded each of 24 gels with equal-sized samples (200 mug protein from pooled rat brain, pH 4-7, stained with ruthenium fluorescent stain for v...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200701074
更新日期:2008-05-01 00:00:00
abstract::In recent years, standardization and quality control have become important key points in industry, e.g. in drug discovery and for developing medical products. Is quality control in academic Proteomics a minor problem nowadays, where standard data formats and public repositories for data sharing exist? In this article,...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000441
更新日期:2011-03-01 00:00:00
abstract::Over the past decade, considerable progress has been made with respect to the analytical methods for analysis of glycans from biological sources. Regardless of the specific methods that are used, glycan analysis includes isolation, identification, and quantitation. Derivatization is indispensable to increase their ide...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201500266
更新日期:2016-01-01 00:00:00
abstract::Human colostrum is an important source of protective, nutritional and developmental factors for the newborn. We have investigated the low abundance proteins in the aqueous phase of human colostrum, after depletion of the major proteins secretory IgA, lactoferrin, alpha-lactalbumin and HSA by immunoabsorption, using 2-...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500558
更新日期:2006-04-01 00:00:00
abstract::Leishmaniasis is a zoonotic disease caused by the species of the genus Leishmania, flagellated protozoa that multiply inside mammalian macrophages and are transmitted by the bite of the sandfly. The disease is widespread and due to the lack of fully effective treatment and vaccination the search for new drugs and immu...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600101
更新日期:2006-07-01 00:00:00
abstract::Pancreatic cancer is the most lethal of all the common malignancies. Markers for early detection of this disease are urgently needed. Here, we optimized and applied a proteome analysis of human pancreatic juice to identify biomarkers for pancreatic cancer. Pancreatic juice samples, devoid of blood or bile contaminatio...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600086
更新日期:2007-04-01 00:00:00
abstract::Seed oil bodies (OBs) are intracellular particles storing lipids as food or biofuel reserves in oleaginous plants. Since Brassica napus OBs could be easily contaminated with protein bodies and/or myrosin cells, they must be purified step by step using floatation technique in order to remove non-specifically trapped pr...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800449
更新日期:2009-06-01 00:00:00
abstract::Prior to analysis by mass spectrometry, protein samples are often digested. Maximizing the peptide yield from digestion can increase the number of peptides detected and the confidence in protein identification. To determine the optimal conditions for digestion, the Michaelis-Menten kinetic parameters for Promega seque...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401268
更新日期:2005-06-01 00:00:00
abstract::Quantitative proteomics is the comparison of distinct proteomes which enables the identification of protein species which exhibit changes in expression or post-translational state in response to a given stimulus. Many different quantitative techniques are being utilized and generate large datasets. Independent of the ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700683
更新日期:2007-09-01 00:00:00
abstract::Several lines of evidence suggest that hnRNPs A/B (hnRNPs A1, A2/B1, and A3) play an important role in proliferation, although the functional overlap among members of hnRNPs A/B remains largely unknown. In this study, we have employed RNAi knockdown and proteomic approaches to investigate the biological functions of h...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300549
更新日期:2014-06-01 00:00:00
abstract::The 26S proteasome is a multicatalytic protease complex that degrades ubiquitinated proteins in eukaryotic cells. It consists of a proteolytic core (the 20S proteasome) as well as regulatory particles, which contain six ATPase (Rpt) subunits involved in unfolding and translocation of substrates to the catalytic chambe...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300207
更新日期:2013-11-01 00:00:00
abstract::The senescence-accelerated mouse (SAM) is a useful animal model to study aging or age-associated disorders due to its inherited aging phenotype. To investigate proteins involved in the aging process in liver, we compared the young (4- or 20-week old) and the aged group (50-week-old) of SAMP8 (short life span) and SAMR...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300562
更新日期:2003-10-01 00:00:00
abstract::Proteins determine the quality of barley in malting and brewing end-uses. In this regard, water-soluble barley proteins play a major role in the formation, stability, and texture of head foams. Our objective was to survey the barley seed proteins that could be involved in the foaming properties of beer. Therefore, two...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401153
更新日期:2005-07-01 00:00:00
abstract::Scab, caused by Fusarium graminearum, is a serious spike disease in wheat. To identify proteins in resistant wheat cultivar Wangshuibai induced by F. graminearum infection, proteins extracted from spikes 6, 12 and 24 h after inoculation were separated by 2-DE. Thirty protein spots showing 3-fold change in abundance wh...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401317
更新日期:2005-11-01 00:00:00
abstract::Recently, several studies employed various proteomic approaches to define diabetes-induced changes in renal proteins. However, functional significance of those datasets in diabetic nephropathy remained unclear. We thus performed integrative proteome network analysis of such datasets followed by various targeted functi...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201700151
更新日期:2017-09-01 00:00:00
abstract::Identification and analysis of types of biological protein-protein interactions and their interfaces to predict obligate and non-obligate complexes is a problem that has drawn the attention of the research community in the past few years. In this paper, we propose a prediction approach to predict these two types of co...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100186
更新日期:2011-10-01 00:00:00