QconCAT standard for calibration of ion mobility-mass spectrometry systems.

Abstract:

:Ion mobility-mass spectrometry (IM-MS) is a useful technique for determining information about analyte ion conformation in addition to mass/charge ratio. The physical principles that govern the mobility of an ion through a gas in the presence of a uniform electric field are well understood, enabling rotationally averaged collision cross sections (Ω) to be directly calculated from measured drift times under well-defined experimental conditions. However, such "first principle" calculations are not straightforward for Traveling Wave (T-Wave) mobility separations due to the range of factors that influence ion motion through the mobility cell. If collision cross section information is required from T-Wave mobility separations, then calibration of the instruments using known standards is essential for each set of experimental conditions. To facilitate such calibration, we have designed and generated an artificial protein based on the QconCAT technology, QCAL-IM, which upon proteolysis can be used as a universal ion mobility calibration standard. This single unique standard enables empirical calculation of peptide ion collision cross sections from the drift time on a T-Wave mobility instrument.

journal_name

J Proteome Res

authors

Chawner R,McCullough B,Giles K,Barran PE,Gaskell SJ,Eyers CE

doi

10.1021/pr3005327

subject

Has Abstract

pub_date

2012-11-02 00:00:00

pages

5564-72

issue

11

eissn

1535-3893

issn

1535-3907

journal_volume

11

pub_type

杂志文章
  • Stage-specific proteome signatures in early bovine embryo development.

    abstract::Development of early embryonic stages before activation of the embryonic genome depends on sufficiently stored products of the maternal genome, adequate recruitment and degradation of mRNAs, as well as activation, deactivation, and relocation of proteins. By application of an isobaric tagging for relative and absolute...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500550t

    authors: Deutsch DR,Fröhlich T,Otte KA,Beck A,Habermann FA,Wolf E,Arnold GJ

    更新日期:2014-10-03 00:00:00

  • Differential N-Glycosylation Patterns in Lung Adenocarcinoma Tissue.

    abstract::To decrease the mortality of lung cancer, better screening and diagnostic tools as well as treatment options are needed. Protein glycosylation is one of the major post-translational modifications that is altered in cancer, but it is not exactly clear which glycan structures are affected. A better understanding of the ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00255

    authors: Ruhaak LR,Taylor SL,Stroble C,Nguyen UT,Parker EA,Song T,Lebrilla CB,Rom WN,Pass H,Kim K,Kelly K,Miyamoto S

    更新日期:2015-11-06 00:00:00

  • Integrity of Glycosylation Processing of a Glycan-Depleted Trimeric HIV-1 Immunogen Targeting Key B-Cell Lineages.

    abstract::Broadly neutralizing antibodies (bNAbs) that target the trimeric HIV-1 envelope glycoprotein spike (Env) are tools that can guide the design of recombinant Env proteins intended to engage the predicted human germline precursors of bNAbs (gl-bNAbs). The protein components of gl-bNAb epitopes are often masked by glycans...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00639

    authors: Behrens AJ,Kumar A,Medina-Ramirez M,Cupo A,Marshall K,Cruz Portillo VM,Harvey DJ,Ozorowski G,Zitzmann N,Wilson IA,Ward AB,Struwe WB,Moore JP,Sanders RW,Crispin M

    更新日期:2018-03-02 00:00:00

  • Minimizing Laboratory-Induced Decay in Bone Proteomics.

    abstract::Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00564

    authors: Procopio N,Buckley M

    更新日期:2017-02-03 00:00:00

  • Solid Digestion of Demineralized Bone as a Method To Access Potentially Insoluble Proteins and Post-Translational Modifications.

    abstract::Bone proteomics is an expanding field for understanding protein changes associated with disease as well as characterizing and detecting proteins preserved in fossil bone. Most previous studies have utilized a protocol with demineralization and extraction approach to isolate and characterize proteins from bone. Through...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00670

    authors: Cleland TP

    更新日期:2018-01-05 00:00:00

  • Highly altered protein expression profile in the adriamycin resistant MCF-7 cell line.

    abstract::The protein expression pattern in the cytosol fraction of the adriamycin resistant MCF-7 cell line (MCF-7/ADR) was compared to that of the parental MCF-7 cell line using two-dimensional gel electrophoresis and mass spectrometry. Twenty proteins with altered abundances were identified and studied in MCF-7/ADR. Both up ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0340577

    authors: Gehrmann ML,Fenselau C,Hathout Y

    更新日期:2004-05-01 00:00:00

  • Comparison of ERLIC-TiO2, HILIC-TiO2, and SCX-TiO2 for global phosphoproteomics approaches.

    abstract::Reversible phosphorylations play a critical role in most biological pathways. Hence, in signaling studies great effort has been put into identification of a maximum number of phosphosites per experiment. Mass spectrometry (MS)-based phosphoproteomics approaches have been proven to be an ideal analytical method for map...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200092z

    authors: Zarei M,Sprenger A,Metzger F,Gretzmeier C,Dengjel J

    更新日期:2011-08-05 00:00:00

  • Characterization of Monophasic Solvent-Based Tissue Extractions for the Detection of Polar Metabolites and Lipids Applying Ultrahigh-Performance Liquid Chromatography-Mass Spectrometry Clinical Metabolic Phenotyping Assays.

    abstract::Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and nonpolar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (hi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00660

    authors: Southam AD,Pursell H,Frigerio G,Jankevics A,Weber RJM,Dunn WB

    更新日期:2021-01-01 00:00:00

  • Shotgun Proteomics and Quantitative Pathway Analysis of the Mechanisms of Action of Dehydroeffusol, a Bioactive Phytochemical with Anticancer Activity from Juncus effusus.

    abstract::Dehydroeffusol (DHE) is a phenanthrene isolated from the Chinese medicinal plant Juncus effusus. Biological evaluation of DHE reveals in vitro and in vivo anticancer effects. We performed a shotgun proteomic analysis using liquid chromatography-tandem mass spectrometry to investigate the changes in the protein profile...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00227

    authors: Chang IS,Sy LK,Cao B,Lum CT,Kwong WL,Fung YE,Lok CN,Che CM

    更新日期:2018-07-06 00:00:00

  • Allostasis and Resilience of the Human Individual Metabolic Phenotype.

    abstract::The urine metabotype of 12 individuals was followed over a period of 8-10 years, which provided the longest longitudinal study of metabolic phenotypes to date. More than 2000 NMR metabolic profiles were analyzed. The majority of subjects have a stable metabotype. Subjects who were exposed to important pathophysiologic...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00275

    authors: Ghini V,Saccenti E,Tenori L,Assfalg M,Luchinat C

    更新日期:2015-07-02 00:00:00

  • Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes.

    abstract::High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00419

    authors: Li H,Gordon SM,Zhu X,Deng J,Swertfeger DK,Davidson WS,Lu LJ

    更新日期:2015-08-07 00:00:00

  • A two-dimensional array for simultaneous sequencing of N- and o-glycans and their glycoforms on specific glycosylation sites.

    abstract::Glycans play major roles in living organisms. Thus, essential information is required on diverse glycans, their location, and moieties in proteins, as well as for technology in a high-throughput manner, for improving functional glycomics. In the present study, we describe a new approach involving a 2-D array, which ha...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070392+

    authors: Tzur Y,Markovich A,Lichtenstein RG

    更新日期:2008-03-01 00:00:00

  • XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

    abstract::As large-scale cross-linking data becomes available, new software tools for data processing and visualization are required to replace manual data analysis. XLink-DB serves as a data storage site and visualization tool for cross-linking results. XLink-DB accepts data generated with any cross-linker and stores them in a...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr301162j

    authors: Zheng C,Weisbrod CR,Chavez JD,Eng JK,Sharma V,Wu X,Bruce JE

    更新日期:2013-04-05 00:00:00

  • Proteomic analysis of hepatitis C virus (HCV) core protein transfection and host regulator PA28γ knockout in HCV pathogenesis: a network-based study.

    abstract::Hepatitis C virus (HCV) causes chronic liver disease worldwide. HCV Core protein (Core) forms the viral capsid and is crucial for HCV pathogenesis and HCV-induced hepatocellular carcinoma, through its interaction with the host factor proteasome activator PA28γ. Here, using BD-PowerBlot high-throughput Western array, w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300121a

    authors: Tripathi LP,Kambara H,Moriishi K,Morita E,Abe T,Mori Y,Chen YA,Matsuura Y,Mizuguchi K

    更新日期:2012-07-06 00:00:00

  • Large-scale identification of core-fucosylated glycopeptide sites in pancreatic cancer serum using mass spectrometry.

    abstract::Glycosylation has significant effects on protein function and cell metastasis, which are important in cancer progression. It is of great interest to identify site-specific glycosylation in search of potential cancer biomarkers. However, the abundance of glycopeptides is low compared to that of nonglycopeptides after t...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00068

    authors: Tan Z,Yin H,Nie S,Lin Z,Zhu J,Ruffin MT,Anderson MA,Simeone DM,Lubman DM

    更新日期:2015-04-03 00:00:00

  • Comparative proteome cataloging of Lactobacillus rhamnosus strains GG and Lc705.

    abstract::The present study reports an in-depth proteome analysis of two Lactobacillus rhamnosus strains, the well-known probiotic strain GG and the dairy strain Lc705. We used GeLC-MS/MS, in which proteins are separated using 1-DE and identified using nanoLC-MS/MS, to generate high-quality protein catalogs. To maximize the num...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr2000896

    authors: Savijoki K,Lietzén N,Kankainen M,Alatossava T,Koskenniemi K,Varmanen P,Nyman TA

    更新日期:2011-08-05 00:00:00

  • Protein-protein recognition control by modulating electrostatic interactions.

    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

    authors: Han S,Yin S,Yi H,Mouhat S,Qiu S,Cao Z,Sabatier JM,Wu Y,Li W

    更新日期:2010-06-04 00:00:00

  • Proteomic Analysis of Brain and Cerebrospinal Fluid from the Three Major Forms of Neuronal Ceroid Lipofuscinosis Reveals Potential Biomarkers.

    abstract::Clinical trials have been conducted for the neuronal ceroid lipofuscinoses (NCLs), a group of neurodegenerative lysosomal diseases that primarily affect children. Whereas clinical rating systems will evaluate long-term efficacy, biomarkers to measure short-term response to treatment would be extremely valuable. To ide...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00460

    authors: Sleat DE,Tannous A,Sohar I,Wiseman JA,Zheng H,Qian M,Zhao C,Xin W,Barone R,Sims KB,Moore DF,Lobel P

    更新日期:2017-10-06 00:00:00

  • Effects of Dietary Different Doses of Copper and High Fructose Feeding on Rat Fecal Metabolome.

    abstract::The gut microbiota plays a critical role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). Increased fructose consumption and inadequate copper intake are two critical risk factors in the development of NAFLD. To gain insight into the role of gut microbiota, fecal metabolites, obtained from rats exposed...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00596

    authors: Wei X,Song M,Yin X,Schuschke DA,Koo I,McClain CJ,Zhang X

    更新日期:2015-09-04 00:00:00

  • Proteomic Analysis of Human Tendon and Ligament: Solubilization and Analysis of Insoluble Extracellular Matrix in Connective Tissues.

    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

    authors: Sato N,Taniguchi T,Goda Y,Kosaka H,Higashino K,Sakai T,Katoh S,Yasui N,Sairyo K,Taniguchi H

    更新日期:2016-12-02 00:00:00

  • An informatics-assisted label-free quantitation strategy that depicts phosphoproteomic profiles in lung cancer cell invasion.

    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 an...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100394u

    authors: Wang YT,Tsai CF,Hong TC,Tsou CC,Lin PY,Pan SH,Hong TM,Yang PC,Sung TY,Hsu WL,Chen YJ

    更新日期:2010-11-05 00:00:00

  • Validation of endogenous peptide identifications using a database of tandem mass spectra.

    abstract::The SwePep database is designed for endogenous peptides and mass spectrometry. It contains information about the peptides such as mass, pl, precursor protein and potential post-translational modifications. Here, we have improved and extended the SwePep database with tandem mass spectra, by adding a locally curated ver...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr800036d

    authors: Fälth M,Svensson M,Nilsson A,Sköld K,Fenyö D,Andren PE

    更新日期:2008-07-01 00:00:00

  • Retinal proteome analysis in a mouse model of oxygen-induced retinopathy.

    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

    authors: Kim SJ,Jin J,Kim YJ,Kim Y,Yu HG

    更新日期:2012-11-02 00:00:00

  • Site-specific quantitative analysis of overglycosylation of collagen in osteogenesis imperfecta using hydrazide chemistry and SILAC.

    abstract::We recently developed a novel method for analysis of collagen O-glycosylations, which include galactosyl-hydroxylysine (GHL) and glucosyl-galactosyl-hydroxylysine (GGHL), using hydrazide chemistry (Taga, Y., Mol. Cell. Proteomics 2012, 11 (6), M111.010397). Here we investigated an overglycosylation model of collagen p...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400079d

    authors: Taga Y,Kusubata M,Ogawa-Goto K,Hattori S

    更新日期:2013-05-03 00:00:00

  • Human Metabolome Changes after a Single Dose of 3,4-Methylenedioxymethamphetamine (MDMA) with Special Focus on Steroid Metabolism and Inflammation Processes.

    abstract::The intake of 3,4-methylenedioxymethamphetamine (MDMA) is known to increase several endogenous substances involved in steroid and inflammation pathways. Untargeted metabolomics screening approaches can determine biochemical changes after drug exposure and can reveal new pathways, which might be involved in the pharmac...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.8b00438

    authors: Boxler MI,Streun GL,Liechti ME,Schmid Y,Kraemer T,Steuer AE

    更新日期:2018-08-03 00:00:00

  • Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition.

    abstract::To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, incl...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr8006478

    authors: Keshamouni VG,Jagtap P,Michailidis G,Strahler JR,Kuick R,Reka AK,Papoulias P,Krishnapuram R,Srirangam A,Standiford TJ,Andrews PC,Omenn GS

    更新日期:2009-01-01 00:00:00

  • Integrative Analysis of Subcellular Quantitative Proteomics Studies Reveals Functional Cytoskeleton Membrane-Lipid Raft Interactions in Cancer.

    abstract::Lipid rafts are dynamic membrane microdomains that orchestrate molecular interactions and are implicated in cancer development. To understand the functions of lipid rafts in cancer, we performed an integrated analysis of quantitative lipid raft proteomics data sets modeling progression in breast cancer, melanoma, and ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b01035

    authors: Shah AD,Inder KL,Shah AK,Cristino AS,McKie AB,Gabra H,Davis MJ,Hill MM

    更新日期:2016-10-07 00:00:00

  • Targeted Metabolic Profiling of the Tg197 Mouse Model Reveals Itaconic Acid as a Marker of Rheumatoid Arthritis.

    abstract::Rheumatoid arthritis is a progressive, highly debilitating disease where early diagnosis, enabling rapid clinical intervention, would provide obvious benefits to patients, healthcare systems, and society. Novel biomarkers that enable noninvasive early diagnosis of the onset and progression of the disease provide one r...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00654

    authors: Michopoulos F,Karagianni N,Whalley NM,Firth MA,Nikolaou C,Wilson ID,Critchlow SE,Kollias G,Theodoridis GA

    更新日期:2016-12-02 00:00:00

  • Epsilon-Q: An Automated Analyzer Interface for Mass Spectral Library Search and Label-Free Protein Quantification.

    abstract::Mass spectrometry (MS) is a widely used proteome analysis tool for biomedical science. In an MS-based bottom-up proteomic approach to protein identification, sequence database (DB) searching has been routinely used because of its simplicity and convenience. However, searching a sequence DB with multiple variable modif...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b01019

    authors: Cho JY,Lee HJ,Jeong SK,Paik YK

    更新日期:2017-12-01 00:00:00

  • Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications.

    abstract::Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00778

    authors: Zhang J,Peng Q,Zhao W,Sun W,Yang J,Liu N

    更新日期:2021-01-01 00:00:00