Abstract：
:Today's highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda , is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Dorfer V,Pichler P,Stranzl T,Stadlmann J,Taus T,Winkler S,Mechtler Kdoi
10.1021/pr500202esubject
Has Abstractpub_date
2014-08-01 00:00:00pages
3679-84issue
8eissn
1535-3893issn
1535-3907journal_volume
13pub_type
杂志文章abstract：:We report the use of chemical derivatization with MALDI-MS/MS analysis for de novo sequence analysis. Using three frequently used homology-based search algorithms, we were able to identify more than 40 proteins from banana, a nonmodel plant with unsequenced genome. Furthermore, this approach allowed the identification...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0601943
更新日期：2007-01-01 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：:Rapid early triage and dose estimation is vital for limited medical resource allocation and treatment of a large number of the wounded after radiological accidents. Lipidomics has been utilized to delineate biofluid lipid signatures after irradiation. Here, high-coverage targeted lipidomics was employed to screen radi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00560
更新日期：2021-01-01 00:00:00
abstract：:Lung cancer, with its high metastatic potential and high mortality rate, is the worldwide leading cause of cancer-related deaths. High-throughput "omics"-based platforms have accelerated the discovery of biomarkers for lung cancer, and the resulting candidates are to be evaluated for their diagnostic potential as noni...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5010828
更新日期：2015-03-06 00:00:00
abstract：:Thermobifida fusca, a thermophilic bacterium belonging to Actinobacteria, is a major degrader of plant cell walls. The protein profiles of the secretome produced by T. fusca grown in cellulose, lignin, and mixture of cellulose and lignin containing culture media, promoting production of respective substrate hydrolyzin...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr901174z
更新日期：2010-06-04 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：:In the past few years, the focus of phosphoproteomics has shifted from merely qualitative to quantitative and targeted studies. Tryptic digestion is a critical step that directly affects quantification and that can be impaired by phosphorylation. Therefore, we systematically characterized the digestion efficiency of 1...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr401181y
更新日期：2014-06-06 00:00:00
abstract：:The gene transfer agent of Rhodobacter capsulatus (GTA) is a unique phage-like particle that exchanges genetic information between members of this same species of bacterium. Besides being an excellent tool for genetic mapping, the GTA has a number of advantages for biotechnological and nanoengineering purposes. To fac...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8006045
更新日期：2009-02-01 00:00:00
abstract：:To identify proteins that are involved in the molecular mechanisms of oxygen-induced retinopathy (OIR), a well-established model of blinding ischemic retinopathy, we quantitatively analyzed the retinal proteome in a mouse model of OIR. OIR was induced by exposing C57BL/6 mice on postnatal day 7 (P7) to 75% hyperoxia f...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300389r
更新日期：2012-11-02 00:00:00
abstract：:Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200323a
更新日期：2011-10-07 00:00:00
abstract：:14-3-3s are phosphoserine/phosphotreonine binding proteins that play pivotal roles as regulators of multiple cellular processes in eukaryotes. The flagellated protozoan parasite Giardia duodenalis, the causing agent of giardiasis, is a valuable simplified eukaryotic model. A single 14-3-3 isoform (g14-3-3) is expresse...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3000199
更新日期：2012-05-04 00:00:00
abstract：:Cooperia oncophora is one of the most common intestinal parasitic nematodes in cattle worldwide. To date, C. oncophora infections are treated using broad-spectrum anthelmintics. However, during the past decade, reports of anthelmintic resistance in this parasite species have emerged worldwide, necessitating new avenue...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400114y
更新日期：2013-09-06 00:00:00
abstract：:Russell and colleagues deserve credit for being the first to use a QconCAT standard to simultaneously quantify both the wild-type and mutant peptides of a protein (i.e., CYP2B6) ( J. Proteome Res. 2013, 12 (12), 5934-5942. DOI: 10.1021/pr400279u). However, the rationale of their study was entirely different from ours ...
journal_title：Journal of proteome research
pub_type： 评论,杂志文章
doi：10.1021/acs.jproteome.8b00940
更新日期：2019-03-01 00:00:00
abstract：:Nanobacteria may cause peripheral neuropathy by adhesion to the perineurium. This hypothesis receives support from five independent observations: (1) identification of perineurial apatite in diabetic patients with peripheral neuropathy, (2) massive presence of nanobacteria in a diabetic patient, (3) beneficial effect ...
journal_title：Journal of proteome research
pub_type： 信件
doi：10.1021/pr049935v
更新日期：2004-09-01 00:00:00
abstract：:In this study, a tandem LC-MS (Waters Xevo TQ) MRM-based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The develop...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1011119
更新日期：2011-04-01 00:00:00
abstract：:Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-thr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008252
更新日期：2008-04-01 00:00:00
abstract：:The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the c...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060367o
更新日期：2007-01-01 00:00:00
abstract：:Arctic ground squirrels provide a unique model to investigate metabolic responses to hibernation in mammals. During winter months these rodents are exposed to severe hypothermia, prolonged fasting, and hypoxemia. In the light of their role in oxygen transport/off-loading and owing to the absence of nuclei and organell...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00018
更新日期：2019-04-05 00:00:00
abstract：:Oxidation generates multiple diverse post-translational modifications resulting in changes in protein structure and function associated with a wide range of diseases. Of these modifications, carbonylations have often been used as hallmarks of oxidative damage. However, accumulating evidence supports the hypothesis tha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00330
更新日期：2017-11-03 00:00:00
abstract：:In-source fragmentation occurs as a byproduct of electrospray ionization. We find that ions produced as a result of in-source fragmentation often match fragment ions produced during MS/MS fragmentation, and we take advantage of this phenomenon in a novel algorithm to analyze LC-MS metabolomics data sets. Our approach ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00601
更新日期：2019-02-01 00:00:00
abstract：:Hepatocellular carcinoma (HCC) is a major liver malignancy possessing a high mortality rate and is particularly prevalent in China and Asia. While surgery is the most effective treatment for liver tumor, about 80% of HCC patients are inoperable at presentation and die early due to late diagnosis. For early cancer dete...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr9002118
更新日期：2010-01-01 00:00:00
abstract：:In this paper, we describe a method for analyzing large-volume protein samples using capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF). To improve the stacking and separation efficiencies of proteins, we added either 0.01% sodium dodecyl sulfate (SDS) or 0.01% poly(ethylene ox...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050298y
更新日期：2006-02-01 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：:A challenge in proteomics is that many observations are missing with the probability of missingness increasing as abundance decreases. Adjusting for this informative missingness is required to assess accurately which proteins are differentially abundant. We propose an empirical Bayesian random censoring threshold (EBR...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500171u
更新日期：2014-09-05 00:00:00
abstract：:Large-scale identification of protein-protein interactions (PPIs) in functional complexes represents an efficient route to elucidate the regulatory rules of cellular functions. Whereas many methods have been developed to identify the PPIs associated with particular target/bait protein in complexes, little information ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800662x
更新日期：2009-05-01 00:00:00
abstract：:The ability to distinguish between phosphopeptides of high and low stoichiometry is essential to discover the true extent of protein phosphorylation. We here extend the strategy whereby a peptide sample is briefly split in two identical parts and differentially labeled preceding the phosphatase treatment of one part. ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500889v
更新日期：2015-02-06 00:00:00
abstract：:To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4009018
更新日期：2014-01-03 00:00:00
abstract：:Src family kinases (SFKs) are the earliest known family of tyrosine kinases and are widely thought to play essential roles in cellular signal transduction. Although numerous functional analyses have been performed, no study has analyzed the specificity of all SFKs on an equal platform. To gain a better understanding o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100773t
更新日期：2010-11-05 00:00:00
abstract：:The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00654
更新日期：2020-11-06 00:00:00
abstract：:We describe Peptoonist, a program that can automatically identify the glycans (sugars) present at each N-glycosylation site of a protein. The input to Peptoonist is a series of mass spectra, both MS and MS/MS, obtained from a liquid chromatography (LC) run of proteolytically digested purified glycoproteins. The progra...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070239f
更新日期：2007-10-01 00:00:00
