当前位置： SCI文献检索 > PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA期刊下所有文献 > IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts.

IonStar enables high-precision, low-missing-data proteomics quantification in large biological cohorts.

Abstract：

:Reproducible quantification of large biological cohorts is critical for clinical/pharmaceutical proteomics yet remains challenging because most prevalent methods suffer from drastically declined commonly quantified proteins and substantially deteriorated quantitative quality as cohort size expands. MS2-based data-independent acquisition approaches represent tremendous advancements in reproducible protein measurement, but often with limited depth. We developed IonStar, an MS1-based quantitative approach enabling in-depth, high-quality quantification of large cohorts by combining efficient/reproducible experimental procedures with unique data-processing components, such as efficient 3D chromatographic alignment, sensitive and selective direct ion current extraction, and stringent postfeature generation quality control. Compared with several popular label-free methods, IonStar exhibited far lower missing data (0.1%), superior quantitative accuracy/precision [∼5% intragroup coefficient of variation (CV)], the widest protein abundance range, and the highest sensitivity/specificity for identifying protein changes (<5% false altered-protein discovery) in a benchmark sample set (n = 20). We demonstrated the usage of IonStar by a large-scale investigation of traumatic injuries and pharmacological treatments in rat brains (n = 100), quantifying >7,000 unique protein groups (>99.8% without missing data across the 100 samples) with a low false discovery rate (FDR), two or more unique peptides per protein, and high quantitative precision. IonStar represents a reliable and robust solution for precise and reproducible protein measurement in large cohorts.

journal_name

Proc Natl Acad Sci U S A

journal_title

Proceedings of the National Academy of Sciences of the United States of America

authors

Shen X,Shen S,Li J,Hu Q,Nie L,Tu C,Wang X,Poulsen DJ,Orsburn BC,Wang J,Qu J

doi

10.1073/pnas.1800541115

subject

Has Abstract

pub_date

2018-05-22 00:00:00

pages

E4767-E4776

issue

21

eissn

0027-8424

issn

1091-6490

pii

1800541115

journal_volume

115

pub_type

杂志文章

相关文献

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA文献大全
  • Logistical feasibility and potential benefits of a population-wide passive-immunotherapy program during an influenza pandemic.

    abstract：:Treatment strategies for severe cases of pandemic influenza have focused on antiviral therapies. In contrast, passive immunotherapy with convalescent blood products has received limited attention. We consider the hypothesis that a passive-immunotherapy program that collects plasma from a small percentage of recovered ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0911596107

    authors： Wu JT,Lee CK,Cowling BJ,Yuen KY

    更新日期：2010-02-16 00:00:00

  • A new tubulin-binding site and pharmacophore for microtubule-destabilizing anticancer drugs.

    abstract：:The recent success of antibody-drug conjugates (ADCs) in the treatment of cancer has led to a revived interest in microtubule-destabilizing agents. Here, we determined the high-resolution crystal structure of the complex between tubulin and maytansine, which is part of an ADC that is approved by the US Food and Drug A...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1408124111

    authors： Prota AE,Bargsten K,Diaz JF,Marsh M,Cuevas C,Liniger M,Neuhaus C,Andreu JM,Altmann KH,Steinmetz MO

    更新日期：2014-09-23 00:00:00

  • Myofibrillogenesis visualized in living embryonic cardiomyocytes.

    abstract：:Myofibril formation was visualized in cultured live cardiomyocytes that were transfected with plasmids expressing green fluorescent protein (GFP) linked to the Z-band protein, alpha-actinin. The expression of this fluorescent protein provided an in vivo label for structures containing alpha-actinin. The GFP-alpha-acti...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.94.17.9493

    authors： Dabiri GA,Turnacioglu KK,Sanger JM,Sanger JW

    更新日期：1997-08-19 00:00:00

  • Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel.

    abstract：:The M2 protein of influenza A virus forms a transmembrane proton channel important for viral infection and replication. Amantadine blocks this channel, thus inhibiting viral replication. Elucidating the high-resolution structure of the M2 protein and its change upon amantadine binding is crucial for designing antivira...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0711500105

    authors： Cady SD,Hong M

    更新日期：2008-02-05 00:00:00

  • Characterization of an almost full-length cDNA coding for human blood coagulation factor X.

    abstract：:A human liver cDNA library was screened by colony hybridization with a bovine factor X cDNA probe. Three of the positive plasmids contained overlapping DNA that coded for most of human factor X mRNA. DNA sequence analysis of these three clones allowed the prediction of the complete amino acid sequence of plasma factor...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.82.11.3591

    authors： Fung MR,Hay CW,MacGillivray RT

    更新日期：1985-06-01 00:00:00

  • Long-term and homogeneous regulation of the Escherichia coli araBAD promoter by use of a lactose transporter of relaxed specificity.

    abstract：:Expression systems based on the Escherichia coli arabinose operon P(BAD) promoter exhibit the all-or-nothing (autocatalytic) induction of expression that was first documented in the lac operon. Under conditions of subsaturating levels of inducer, some of the cells of the population are fully induced, whereas other cel...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.122227599

    authors： Morgan-Kiss RM,Wadler C,Cronan JE Jr

    更新日期：2002-05-28 00:00:00

  • Tat protein of human immunodeficiency virus type 1 represses expression of manganese superoxide dismutase in HeLa cells.

    abstract：:Using a HeLa cell line stably transfected with the tat gene from human immunodeficiency virus type 1, we have found that the expression of the regulatory Tat protein suppresses the expression of cellular Mn-containing superoxide dismutase (Mn-SOD). This enzyme is one of the cell's primary defenses against oxygen-deriv...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.90.16.7632

    authors： Flores SC,Marecki JC,Harper KP,Bose SK,Nelson SK,McCord JM

    更新日期：1993-08-15 00:00:00

  • Reprogramming responsiveness to checkpoint blockade in dysfunctional CD8 T cells.

    abstract：:Established T cell dysfunction is a barrier to antitumor responses, and checkpoint blockade presumably reverses this. Many patients fail to respond to treatment and/or develop autoimmune adverse events. The underlying reason for T cell responsiveness remains elusive. Here, we show that susceptibility to checkpoint blo...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1810326116

    authors： Nelson CE,Mills LJ,McCurtain JL,Thompson EA,Seelig DM,Bhela S,Quarnstrom CF,Fife BT,Vezys V

    更新日期：2019-02-12 00:00:00

  • Myelination of peripheral nerves is controlled by PI4KB through regulation of Schwann cell Golgi function.

    abstract：:Better understanding myelination of peripheral nerves would benefit patients affected by peripheral neuropathies, including Charcot-Marie-Tooth disease. Little is known about the role the Golgi compartment plays in Schwann cell (SC) functions. Here, we studied the role of Golgi in myelination of peripheral nerves in m...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.2007432117

    authors： Baba T,Alvarez-Prats A,Kim YJ,Abebe D,Wilson S,Aldworth Z,Stopfer MA,Heuser J,Balla T

    更新日期：2020-11-10 00:00:00

  • How subunit coupling produces the gamma-subunit rotary motion in F1-ATPase.

    abstract：:F(o)F(1)-ATP synthase manufactures the energy "currency," ATP, of living cells. The soluble F(1) portion, called F(1)-ATPase, can act as a rotary motor, with ATP binding, hydrolysis, and product release, inducing a torque on the gamma-subunit. A coarse-grained plastic network model is used to show at a residue level o...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0708746105

    authors： Pu J,Karplus M

    更新日期：2008-01-29 00:00:00

  • Purification of tropomyosin from Saccharomyces cerevisiae and identification of related proteins in Schizosaccharomyces and Physarum.

    abstract：:Tropomyosin is a key component of the contractile systems found in muscle and nonmuscle cells of higher eukaryotes. Based on properties common to all tropomyosins, we have purified a protein from Saccharomyces cerevisiae that resembles tropomyosins from higher cells. The yeast protein remains soluble after heat treatm...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.86.1.90

    authors： Liu HP,Bretscher A

    更新日期：1989-01-01 00:00:00

  • Peroxynitrite inhibition of Coxsackievirus infection by prevention of viral RNA entry.

    abstract：:Although peroxynitrite is harmful to the host, the beneficial effects of peroxynitrite are less well understood. We explored the role of peroxynitrite in the host immune response to Coxsackievirus infection. Peroxynitrite inhibits viral replication in vitro, in part by inhibiting viral RNA entry into the host cell. Ni...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0400518101

    authors： Padalko E,Ohnishi T,Matsushita K,Sun H,Fox-Talbot K,Bao C,Baldwin WM 3rd,Lowenstein CJ

    更新日期：2004-08-10 00:00:00

  • Plasminogen activator production accompanies loss of anchorage regulation in transformation of primary rat embryo cells by simian virus 40.

    abstract：:We have isolated several lines of rat embryo cells transformed by simian virus 40. All these lines are fully transformed with regard to saturation density and serum sensitivity, but they differ greatly in their anchorage dependence, as assayed by efficiency of plating in methyl cellulose suspension. This set of lines ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.71.12.4792

    authors： Pollack R,Risser R,Conlon S,Rifkin D

    更新日期：1974-12-01 00:00:00

  • Spoken word production: a theory of lexical access.

    abstract：:A core operation in speech production is the preparation of words from a semantic base. The theory of lexical access reviewed in this article covers a sequence of processing stages beginning with the speaker's focusing on a target concept and ending with the initiation of articulation. The initial stages of preparatio...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.231459498

    authors： Levelt WJ

    更新日期：2001-11-06 00:00:00

  • Severe iron deficiency anemia in transgenic mice expressing liver hepcidin.

    abstract：:We recently reported the hemochromatosis-like phenotype observed in our Usf2 knockout mice. In these mice, as in murine models of hemochromatosis and patients with hereditary hemochromatosis, iron accumulates in parenchymal cells (in particular, liver and pancreas), whereas the reticuloendothelial system is spared fro...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.072632499

    authors： Nicolas G,Bennoun M,Porteu A,Mativet S,Beaumont C,Grandchamp B,Sirito M,Sawadogo M,Kahn A,Vaulont S

    更新日期：2002-04-02 00:00:00

  • Terminal differentiation and calcification in rabbit chondrocyte cultures grown in centrifuge tubes: regulation by transforming growth factor beta and serum factors.

    abstract：:Rabbit chondrocyte cultures on plastic dishes are capable of depositing a cartilaginous matrix, although the matrix does not calcify unless high levels of phosphate are added to the medium. In the present study, we cultivated a pelleted mass of rabbit growth-plate chondrocytes in the presence of Eagle's minimum essent...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.85.24.9552

    authors： Kato Y,Iwamoto M,Koike T,Suzuki F,Takano Y

    更新日期：1988-12-01 00:00:00

  • Nucleotide sequence analysis of feline immunodeficiency virus: genome organization and relationship to other lentiviruses.

    abstract：:We determined the complete nucleotide sequence of an infectious proviral molecular clone (FIV-14) of the feline immunodeficiency virus (FIV). FIV-14 has a genome organization similar in complexity to other lentiviruses. In addition to three large open reading frames representing the gag, pol, and env genes, at least f...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.86.20.8088

    authors： Olmsted RA,Hirsch VM,Purcell RH,Johnson PR

    更新日期：1989-10-01 00:00:00

  • Global transcriptome response to ionic liquid by a tropical rain forest soil bacterium, Enterobacter lignolyticus.

    abstract：:To process plant-based renewable biofuels, pretreatment of plant feedstock with ionic liquids has significant advantages over current methods for deconstruction of lignocellulosic feedstocks. However, ionic liquids are often toxic to the microorganisms used subsequently for biomass saccharification and fermentation. W...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1112750109

    authors： Khudyakov JI,D'haeseleer P,Borglin SE,Deangelis KM,Woo H,Lindquist EA,Hazen TC,Simmons BA,Thelen MP

    更新日期：2012-08-07 00:00:00

  • Psychologically induced cooling of a specific body part caused by the illusory ownership of an artificial counterpart.

    abstract：:The sense of body ownership represents a fundamental aspect of our self-awareness, but is disrupted in many neurological, psychiatric, and psychological conditions that are also characterized by disruption of skin temperature regulation, sometimes in a single limb. We hypothesized that skin temperature in a specific l...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0803768105

    authors： Moseley GL,Olthof N,Venema A,Don S,Wijers M,Gallace A,Spence C

    更新日期：2008-09-02 00:00:00

  • Global analysis of LARP1 translation targets reveals tunable and dynamic features of 5' TOP motifs.

    abstract：:Terminal oligopyrimidine (TOP) motifs are sequences at the 5' ends of mRNAs that link their translation to the mTOR Complex 1 (mTORC1) nutrient-sensing signaling pathway. They are commonly regarded as discrete elements that reside on ∼100 mRNAs that mostly encode translation factors. However, the full spectrum of TOP ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1912864117

    authors： Philippe L,van den Elzen AMG,Watson MJ,Thoreen CC

    更新日期：2020-03-10 00:00:00

  • Quon 3D language for quantum information.

    abstract：:We present a 3D topological picture-language for quantum information. Our approach combines charged excitations carried by strings, with topological properties that arise from embedding the strings in the interior of a 3D manifold with boundary. A quon is a composite that acts as a particle. Specifically, a quon is a ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1621345114

    authors： Liu Z,Wozniakowski A,Jaffe AM

    更新日期：2017-03-07 00:00:00

  • Design of stereoselective Ziegler-Natta propene polymerization catalysts.

    abstract：:After five decades of largely serendipitous (albeit formidable) progress, catalyst design in Ziegler-Natta olefin polymerization, i.e., the rational implementation of new active species to target predetermined polyolefin architectures, has ultimately become a realistic ambition, thanks to a much deeper fundamental und...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0602856103

    authors： Busico V,Cipullo R,Pellecchia R,Ronca S,Roviello G,Talarico G

    更新日期：2006-10-17 00:00:00

  • Early onset preeclampsia in a model for human placental trophoblast.

    abstract：:We describe a model for early onset preeclampsia (EOPE) that uses induced pluripotent stem cells (iPSCs) generated from umbilical cords of EOPE and control (CTL) pregnancies. These iPSCs were then converted to placental trophoblast (TB) representative of early pregnancy. Marker gene analysis indicated that both sets o...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1816150116

    authors： Sheridan MA,Yang Y,Jain A,Lyons AS,Yang P,Brahmasani SR,Dai A,Tian Y,Ellersieck MR,Tuteja G,Schust DJ,Schulz LC,Ezashi T,Roberts RM

    更新日期：2019-03-05 00:00:00

  • One-trial associative learning modifies food odor preferences of a terrestrial mollusc.

    abstract：:We present evidence of rapid and reliable associative learning by the terrestrial mollusc, Limax maximus. Slugs were exposed once to a pairing of a highly attractive food odor (potato or carrot) and a saturated solution of quinidine sulfate, a bitter-tasting plant substance. In comparison with control slugs, the expos...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.78.1.640

    authors： Sahley C,Gelperin A,Rudy JW

    更新日期：1981-01-01 00:00:00

  • Mechanical stress compromises multicomponent efflux complexes in bacteria.

    abstract：:Physical forces have a profound effect on growth, morphology, locomotion, and survival of organisms. At the level of individual cells, the role of mechanical forces is well recognized in eukaryotic physiology, but much less is known about prokaryotic organisms. Recent findings suggest an effect of physical forces on b...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1909562116

    authors： Genova LA,Roberts MF,Wong YC,Harper CE,Santiago AG,Fu B,Srivastava A,Jung W,Wang LM,Krzemiński Ł,Mao X,Sun X,Hui CY,Chen P,Hernandez CJ

    更新日期：2019-12-17 00:00:00

  • The degree of extra-pair paternity increases with genetic variability.

    abstract：:The amount of extra-pair paternity in socially monogamous bird species varies from 0% to 76% extra-pair offspring. The causes of this remarkable interspecific variation are largely unknown, although intraspecific analyses suggest that females seek extra-pair matings to improve the genetic quality of their offspring. I...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.95.16.9390

    authors： Petrie M,Doums C,Moller AP

    更新日期：1998-08-04 00:00:00

  • Drosophila IRBP bZIP heterodimer binds P-element DNA and affects hybrid dysgenesis.

    abstract：:In Drosophila, P-element transposition causes mutagenesis and genome instability during hybrid dysgenesis. The P-element 31-bp terminal inverted repeats (TIRs) contain sequences essential for transposase cleavage and have been implicated in DNA repair via protein-DNA interactions with cellular proteins. The identity a...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1613508113

    authors： Francis MJ,Roche S,Cho MJ,Beall E,Min B,Panganiban RP,Rio DC

    更新日期：2016-11-15 00:00:00

  • Tetrodotoxin-sensitive sodium channels in normal human fibroblasts and normal human glia-like cells.

    abstract：:Tetrodotoxin-sensitive sodium channels are detectable in normal human fibroblasts and in "glia-like" cells at appreciable levels when compared to what is observed in established neuronal cell lines in culture. Two- to 3-fold stimulations of sodium influx are observed in the presence of 0.2 mM veratridine and scorpion ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.76.12.6425

    authors： Munson R Jr,Westermark B,Glaser L

    更新日期：1979-12-01 00:00:00

  • Reconstitution of simian virus 40 DNA replication with purified proteins.

    abstract：:Replication of plasmid DNA molecules containing the simian virus 40 (SV40) origin of DNA replication has been reconstituted with seven highly purified cellular proteins plus the SV40 large tumor (T) antigen. Initiation of DNA synthesis is absolutely dependent upon T antigen, replication protein A, and the DNA polymera...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.87.22.8692

    authors： Weinberg DH,Collins KL,Simancek P,Russo A,Wold MS,Virshup DM,Kelly TJ

    更新日期：1990-11-01 00:00:00

  • Alteration of neural cell adhesion molecule (N-CAM) expression after neuronal cell transformation by Rous sarcoma virus.

    abstract：:The effect of transformation by Rous sarcoma virus on the neural cell adhesion molecule N-CAM was assessed by immunoblotting, immunofluorescence staining, and an in vitro cell-cell aggregation assay using highly specific antibodies to the adhesion molecule. Expression of N-CAM was found to be temperature dependent in ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.81.3.969

    authors： Greenberg ME,Brackenbury R,Edelman GM

    更新日期：1984-02-01 00:00:00