A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins.


:A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.


J Proteome Res


Hong Q,Ruhaak LR,Stroble C,Parker E,Huang J,Maverakis E,Lebrilla CB




Has Abstract


2015-12-04 00:00:00












  • Heterogeneous nuclear ribonucleoprotein A1 is identified as a potential biomarker for colorectal cancer based on differential proteomics technology.

    abstract::Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Ma YL,Peng JY,Zhang P,Huang L,Liu WJ,Shen TY,Chen HQ,Zhou YK,Zhang M,Chu ZX,Qin HL

    更新日期:2009-10-01 00:00:00

  • An integrated proteomic workflow for two-dimensional differential gel electrophoresis and robotic spot picking.

    abstract::New technologies have advanced the field of proteomics, and a number of companies have developed innovative platforms to drive this research. However, significant challenges are often encountered when trying to integrate complementary technologies from multiple manufacturers. We have developed a software and hardware ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Mahnke RC,Corzett TH,McCutchen-Maloney SL,Chromy BA

    更新日期:2006-09-01 00:00:00

  • Quantitative phosphoproteomic analysis of T cell receptor signaling in diabetes prone and resistant mice.

    abstract::Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the a...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Iwai LK,Benoist C,Mathis D,White FM

    更新日期:2010-06-04 00:00:00

  • The Muscle Metabolome Differs between Healthy and Frail Older Adults.

    abstract::Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the frailty syndrome of aging is loss of skeletal muscle. In this study we assessed the skeletal muscle biopsy metabolome of healthy young, healthy older and frail olde...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Fazelzadeh P,Hangelbroek RW,Tieland M,de Groot LC,Verdijk LB,van Loon LJ,Smilde AK,Alves RD,Vervoort J,Müller M,van Duynhoven JP,Boekschoten MV

    更新日期:2016-02-05 00:00:00

  • Proteomic analysis of multiprotein complexes in the thylakoid membrane upon cadmium treatment.

    abstract::The time course of the thylakoid membranes proteomic profile changes upon cadmium (Cd) addition to hydroponic Spinacia oleracea L. plants has been investigated. Two different proteomic approaches have been used: blue native gel electrophoresis followed by SDS-PAGE (2D BN-SDS-PAGE) and sucrose density gradient ultracen...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Fagioni M,D'Amici GM,Timperio AM,Zolla L

    更新日期:2009-01-01 00:00:00

  • Proteomic analysis of Pinus radiata needles: 2-DE map and protein identification by LC/MS/MS and substitution-tolerant database searching.

    abstract::Pinus radiata is one of the most economically important forest tree species, with a worldwide production of around 370 million m (3) of wood per year. Current selection of elite trees to be used in conservation and breeding programes requires the physiological and molecular characterization of available populations. T...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Valledor L,Castillejo MA,Lenz C,Rodríguez R,Cañal MJ,Jorrín J

    更新日期:2008-07-01 00:00:00

  • 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 avera...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


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

    更新日期:2012-11-02 00:00:00

  • Dynamic omics approach identifies nutrition-mediated microbial interactions.

    abstract::"Omics" studies reported to date have dealt with either thoroughly characterized single species or poorly explored meta-microbial communities. However, these techniques are capable of producing highly informative data for the analysis of interactions between two organisms. We examined the bacterial interaction between...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Nakanishi Y,Fukuda S,Chikayama E,Kimura Y,Ohno H,Kikuchi J

    更新日期:2011-02-04 00:00:00

  • Profiling of glycans in serum for the discovery of potential biomarkers for ovarian cancer.

    abstract::A glycomic approach is developed to identify oligosaccharide markers for ovarian cancer by rapidly profiling globally released oligosaccharides. Glycoproteins shed by cancer cells are found in the supernatant (or conditioned media) of cultured cells. In this approach, shed glycoproteins are profiled for their oligosac...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: An HJ,Miyamoto S,Lancaster KS,Kirmiz C,Li B,Lam KS,Leiserowitz GS,Lebrilla CB

    更新日期:2006-07-01 00:00:00

  • The proapoptotic C16-ceramide-dependent pathway requires the death-promoting factor Btf in colon adenocarcinoma cells.

    abstract::Ceramides are central molecules in sphingolipid metabolism. They are involved in the regulation of cancer-cell growth, differentiation, senescence and apoptosis. To better understand how these secondary messengers induce their biological effects, adenocarcinoma cells (HCT116) were treated with exogenous long-chain cer...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Rénert AF,Leprince P,Dieu M,Renaut J,Raes M,Bours V,Chapelle JP,Piette J,Merville MP,Fillet M

    更新日期:2009-10-01 00:00:00

  • IDAWG: Metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells.

    abstract::Robust quantification is an essential component of comparative -omic strategies. In this regard, glycomics lags behind proteomics. Although various isotope-tagging and direct quantification methods have recently enhanced comparative glycan analysis, a cell culture labeling strategy, that could provide for glycomics th...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Orlando R,Lim JM,Atwood JA 3rd,Angel PM,Fang M,Aoki K,Alvarez-Manilla G,Moremen KW,York WS,Tiemeyer M,Pierce M,Dalton S,Wells L

    更新日期:2009-08-01 00:00:00

  • Characterization of IQGAP1-containing complexes in NK-like cells: evidence for Rac 2 and RACK1 association during homotypic adhesion.

    abstract::IQGAP1 is a scaffolding protein that binds to a diverse array of signaling and structural molecules that are often associated with cell polarization and adhesion. Through interaction with its target proteins, IQGAP1 participates in multiple cellular functions, including Ca2+-calmodulin signaling, definition of cytoske...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Meng X,Krokhin O,Cheng K,Ens W,Wilkins JA

    更新日期:2007-02-01 00:00:00

  • Quantitative Proteomic Analysis of Small and Large Extracellular Vesicles (EVs) Reveals Enrichment of Adhesion Proteins in Small EVs.

    abstract::Extracellular vesicles (EVs) are important mediators of cell-cell communication due to their cargo content of proteins, lipids, and RNAs. We previously reported that small EVs (SEVs) called exosomes promote directed and random cell motility, invasion, and serum-independent growth. In contrast, larger EVs (LEVs) were n...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Jimenez L,Yu H,McKenzie AJ,Franklin JL,Patton JG,Liu Q,Weaver AM

    更新日期:2019-03-01 00:00:00

  • Global De Novo Protein-Protein Interactome Elucidates Interactions of Drought-Responsive Proteins in Horse Gram (Macrotyloma uniflorum).

    abstract::Inspired by the availability of de novo transcriptome of horse gram (Macrotyloma uniflorum) and recent developments in systems biology studies, the first ever global protein-protein interactome (PPI) map was constructed for this highly drought-tolerant legume. Large-scale studies of PPIs and the constructed database w...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Bhardwaj J,Gangwar I,Panzade G,Shankar R,Yadav SK

    更新日期:2016-06-03 00:00:00

  • Proteomic analysis of hearts from Akita mice suggests that increases in soluble epoxide hydrolase and antioxidative programming are key changes in early stages of diabetic cardiomyopathy.

    abstract::Cardiovascular disease is the leading cause of diabetic morbidity with more than 10% of type 1 diabetes mellitus (T1DM) patients dying before they are 40 years old. This study utilized Akita mice, a murine model with T1DM progression analogous to that of humans. Diabetic cardiomyopathy in Akita mice presents as cardia...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Dewey S,Lai X,Witzmann FA,Sohal M,Gomes AV

    更新日期:2013-09-06 00:00:00

  • Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration.

    abstract::Protein-protein interactions play a major role in the molecular machinery of life, and various techniques such as AP-MS are dedicated to their identification. However, those techniques return lists of proteins devoid of organizational structure, not detailing which proteins interact with which others. Proposing a hier...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Postic G,Marcoux J,Reys V,Andreani J,Vandenbrouck Y,Bousquet MP,Mouton-Barbosa E,Cianférani S,Burlet-Schiltz O,Guerois R,Labesse G,Tufféry P

    更新日期:2020-07-02 00:00:00

  • Quantitative Proteomics Combined with Two Genetic Strategies for Screening Substrates of Ubiquitin Ligase Hrt3.

    abstract::Ubiquitin ligases (E3s) serve as key regulators for the ubiquitylation-mediated pathway. The identification of the corresponding relationship between E3 and its substrates is challenging but required for understanding the regulatory network of ubiquitylation. The low abundance of ubiquitinated conjugates and high redu...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Lan Q,Wang Y,Sun Z,Li Y,Zhang C,Chang L,Gao Y,Wu J,Wang F,Xu P

    更新日期:2020-01-03 00:00:00

  • Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated α-fibrinogen in plasma for pancreatic cancer diagnosis.

    abstract::Pancreatic cancer is a devastating disease and early diagnosis and treatment are essential to improve the prognosis. We previously showed that α-fibrinogen containing hydroxylated proline residues at positions 530 and 565 is increased in plasma of pancreatic cancer patients. However, no antibody specific for hydroxyla...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Yoneyama T,Ohtsuki S,Ono M,Ohmine K,Uchida Y,Yamada T,Tachikawa M,Terasaki T

    更新日期:2013-02-01 00:00:00

  • Quantitative Proteomics of Enriched Esophageal and Gut Tissues from the Human Blood Fluke Schistosoma mansoni Pinpoints Secreted Proteins for Vaccine Development.

    abstract::Schistosomes are blood-dwelling helminth parasites that cause schistosomiasis, a debilitating disease resulting in inflammation and, in extreme cases, multiple organ damage. Major challenges to control the transmission persist, and the discovery of protective antigens remains of critical importance for vaccine develop...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Neves LX,Wilson RA,Brownridge P,Harman VM,Holman SW,Beynon RJ,Eyers CE,DeMarco R,Castro-Borges W

    更新日期:2020-01-03 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


    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

  • Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study.

    abstract::Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Chen M,Zhang M,Zhai L,Hu H,Liu P,Tan M

    更新日期:2017-09-01 00:00:00

  • Circulating Lamin B1 (LMNB1) biomarker detects early stages of liver cancer in patients.

    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


    authors: Sun S,Xu MZ,Poon RT,Day PJ,Luk JM

    更新日期:2010-01-01 00:00:00

  • Proteomic and Glycoproteomic Profilings Reveal That Post-translational Modifications of Toxins Contribute to Venom Phenotype in Snakes.

    abstract::Snake venoms are biological weapon systems composed of secreted proteins and peptides that are used for immobilizing or killing prey. Although post-translational modifications are widely investigated because of their importance in many biological phenomena, we currently still have little understanding of how protein g...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Andrade-Silva D,Zelanis A,Kitano ES,Junqueira-de-Azevedo IL,Reis MS,Lopes AS,Serrano SM

    更新日期:2016-08-05 00:00:00

  • Mitochondrial Function, Metabolic Regulation, and Human Disease Viewed through the Prism of Sirtuin 4 (SIRT4) Functions.

    abstract::As cellular metabolic hubs, mitochondria are the main energy producers for the cell. These organelles host essential energy producing biochemical processes, including the TCA cycle, fatty acid oxidation, and oxidative phosphorylation. An accumulating body of literature has demonstrated that a majority of mitochondrial...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审


    authors: Betsinger CN,Cristea IM

    更新日期:2019-05-03 00:00:00

  • A protein processing filter method for bacterial identification by mass spectrometry-based proteomics.

    abstract::A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposab...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Jabbour RE,Deshpande SV,Stanford MF,Wick CH,Zulich AW,Snyder AP

    更新日期:2011-02-04 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


    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

  • Lysine and Arginine Protein Post-translational Modifications by Enhanced DIA Libraries: Quantification in Murine Liver Disease.

    abstract::Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Robinson AE,Binek A,Venkatraman V,Searle BC,Holewinski RJ,Rosenberger G,Parker SJ,Basisty N,Xie X,Lund PJ,Saxena G,Mato JM,Garcia BA,Schilling B,Lu SC,Van Eyk JE

    更新日期:2020-10-02 00:00:00

  • Evolutionary Characteristics of Missing Proteins: Insights into the Evolution of Human Chromosomes Related to Missing-Protein-Encoding Genes.

    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


    authors: Xu A,Li G,Yang D,Wu S,Ouyang H,Xu P,He F

    更新日期:2015-12-04 00:00:00

  • Urinary metabolite profiling combined with computational analysis predicts interstitial cystitis-associated candidate biomarkers.

    abstract::Interstitial cystitis/painful bladder syndrome (IC) is a chronic syndrome of unknown etiology that presents with bladder pain, urinary frequency, and urgency. The lack of specific biomarkers and a poor understanding of underlying molecular mechanisms present challenges for disease diagnosis and therapy. The goals of t...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Wen H,Lee T,You S,Park SH,Song H,Eilber KS,Anger JT,Freeman MR,Park S,Kim J

    更新日期:2015-01-02 00:00:00

  • Quantitative proteomic analysis of membrane proteins involved in astroglial differentiation of neural stem cells by SILAC labeling coupled with LC-MS/MS.

    abstract::Membrane proteins play a critical role in the process of neural stem cell self-renewal and differentiation. Here, we apply the SILAC (stable isotope labeling by amino acids in cell culture) approach to quantitatively compare the membrane proteome of the self-renewing and the astroglial differentiating cells. High-reso...

    journal_title:Journal of proteome research

    pub_type: 杂志文章


    authors: Cao R,Chen K,Song Q,Zang Y,Li J,Wang X,Chen P,Liang S

    更新日期:2012-02-03 00:00:00