Search Results - "EDDES, James S"

Development and validation of a spectral library searching method for peptide identification from MS/MS by Lam, Henry, Deutsch, Eric W., Eddes, James S., Eng, Jimmy K., King, Nichole, Stein, Stephen E., Aebersold, Ruedi

“…A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods,…”
Get full text

Building consensus spectral libraries for peptide identification in proteomics by Lam, Henry, Deutsch, Eric W, Eddes, James S, Eng, Jimmy K, Stein, Stephen E, Aebersold, Ruedi

“…Spectral searching has drawn increasing interest as an alternative to sequence-database searching in proteomics. We developed and validated an open-source…”
Get full text

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database by Omenn, Gilbert S., States, David J., Adamski, Marcin, Blackwell, Thomas W., Menon, Rajasree, Hermjakob, Henning, Apweiler, Rolf, Haab, Brian B., Simpson, Richard J., Eddes, James S., Kapp, Eugene A., Moritz, Robert L., Chan, Daniel W., Rai, Alex J., Admon, Arie, Aebersold, Ruedi, Eng, Jimmy, Hancock, William S., Hefta, Stanley A., Meyer, Helmut, Paik, Young-Ki, Yoo, Jong-Shin, Ping, Peipei, Pounds, Joel, Adkins, Joshua, Qian, Xiaohong, Wang, Rong, Wasinger, Valerie, Wu, Chi Yue, Zhao, Xiaohang, Zeng, Rong, Archakov, Alexander, Tsugita, Akira, Beer, Ilan, Pandey, Akhilesh, Pisano, Michael, Andrews, Philip, Tammen, Harald, Speicher, David W., Hanash, Samir M.

“…HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS…”
Get full text

Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins by Moritz, Robert L., Clippingdale, Andrew B., Kapp, Eugene A., Eddes, James S., Ji, Hong, Gilbert, Sam, Connolly, Lisa M., Simpson, Richard J.

“…Free‐flow electrophoresis (FFE) and rapid (6 min) RP‐HPLC was used to fractionate human citrate‐treated plasma. Prior to analysis, the six most abundant…”
Get full text

Protein Cross-Linking Analysis Using Mass Spectrometry, Isotope-Coded Cross-Linkers, and Integrated Computational Data Processing by Seebacher, Jan, Mallick, Parag, Zhang, Ning, Eddes, James S, Aebersold, Ruedi, Gelb, Michael H

“…Distance constraints in proteins and protein complexes provide invaluable information for calculation of 3D structures, identification of protein binding…”
Get full text

Matrix-assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin-fixed tissue by Gustafsson, Ove J. R., Eddes, James S., Meding, Stephan, McColl, Shaun R., Oehler, Martin K., Hoffmann, Peter

“…RATIONALE Matrix‐assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the means to map the in situ distribution of tryptic peptides…”
Get full text

The Standard Protein Mix Database: A Diverse Data Set To Assist in the Production of Improved Peptide and Protein Identification Software Tools by Klimek, John, Eddes, James S, Hohmann, Laura, Jackson, Jennifer, Peterson, Amelia, Letarte, Simon, Gafken, Philip R, Katz, Jonathan E, Mallick, Parag, Lee, Hookeun, Schmidt, Alexander, Ossola, Reto, Eng, Jimmy K, Aebersold, Ruedi, Martin, Daniel B

“…Tandem mass spectrometry (MS/MS) is frequently used in the identification of peptides and proteins. Typical proteomic experiments rely on algorithms such as…”
Get full text

Phosphorylation of NS5A Serine-235 is essential to hepatitis C virus RNA replication and normal replication compartment formation by Eyre, Nicholas S, Hampton-Smith, Rachel J, Aloia, Amanda L, Eddes, James S, Simpson, Kaylene J, Hoffmann, Peter, Beard, Michael R

“…Abstract Hepatitis C virus (HCV) NS5A protein is essential for HCV RNA replication and virus assembly. Here we report the identification of NS5A…”
Get full text

Tryptic Peptide Reference Data Sets for MALDI Imaging Mass Spectrometry on Formalin-fixed Ovarian Cancer Tissues by Meding, Stephan, Martin, Karina, Gustafsson, Ove J. R, Eddes, James S, Hack, Sandra, Oehler, Martin K, Hoffmann, Peter

“…MALDI imaging mass spectrometry is a powerful tool for morphology-based proteomic tissue analysis. However, peptide identification is still a major challenge…”
Get full text

Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides by Nesvizhskii, Alexey I, Roos, Franz F, Grossmann, Jonas, Vogelzang, Mathijs, Eddes, James S, Gruissem, Wilhelm, Baginsky, Sacha, Aebersold, Ruedi

“…In mass spectrometry-based proteomics, frequently hundreds of thousands of MS/MS spectra are collected in a single experiment. Of these, a relatively small…”
Get full text

Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS by Gustafsson, Johan O.R., Eddes, James S., Meding, Stephan, Koudelka, Tomas, Oehler, Martin K., McColl, Shaun R., Hoffmann, Peter

“…One of the important challenges for MALDI imaging mass spectrometry (MALDI-IMS) is the unambiguous identification of measured analytes. One way to do this is…”
Get full text

Mining a Tandem Mass Spectrometry Database To Determine the Trends and Global Factors Influencing Peptide Fragmentation by Kapp, Eugene A, Schütz, Frédéric, Reid, Gavin E, Eddes, James S, Moritz, Robert L, O'Hair, Richard A. J, Speed, Terence P, Simpson, Richard J

“…A database of 5500 unique peptide tandem mass spectra acquired in an ion trap mass spectrometer was assembled for peptides derived from proteins digested with…”
Get full text

Proteomic Analyses Using Grifola frondosa Metalloendoprotease Lys-N by Hohmann, Laura, Sherwood, Carly, Eastham, Ashley, Peterson, Amelia, Eng, Jimmy K, Eddes, James S, Shteynberg, David, Martin, Daniel B

“…Proteomic analysis typically has been performed using proteins digested with trypsin because of the excellent fragmentation patterns they produce in collision…”
Get full text

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas by King, Nichole L, Deutsch, Eric W, Ranish, Jeffrey A, Nesvizhskii, Alexey I, Eddes, James S, Mallick, Parag, Eng, Jimmy, Desiere, Frank, Flory, Mark, Martin, Daniel B, Kim, Bong, Lee, Hookeun, Raught, Brian, Aebersold, Ruedi

“…We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to…”
Get full text

Proteomic analysis of the human colon carcinoma cell line (LIM 1215): Development of a membrane protein database by Simpson, Richard J., Connolly, Lisa M., Eddes, James S., Pereira, Joseph J., Moritz, Robert L., Reid, Gavin E.

“…The proteomic definition of plasma membrane proteins is an important initial step in searching for novel tumor marker proteins expressed during the different…”
Get full text

CHOMPER: A bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies by Eddes, James S., Kapp, Eugene A., Frecklington, David F., Connolly, Lisa M., Layton, Meredith J., Moritz, Robert L., Simpson, Richard J.

“…Current efforts aimed at developing high‐throughput proteomics focus on increasing the speed of protein identification. Although improvements in sample…”
Get full text

Dynamic Spectrum Quality Assessment and Iterative Computational Analysis of Shotgun Proteomic Data by Nesvizhskii, Alexey I., Roos, Franz F., Grossmann, Jonas, Vogelzang, Mathijs, Eddes, James S., Gruissem, Wilhelm, Baginsky, Sacha, Aebersold, Ruedi

“…In mass spectrometry-based proteomics, frequently hundreds of thousands of MS/MS spectra are collected in a single experiment. Of these, a relatively small…”
Get full text

Disulfide Bond Structure and N-Glycosylation Sites of the Extracellular Domain of the Human Interleukin-6 Receptor by Cole, Adam R., Hall, Nathan E., Treutlein, Herbert R., Eddes, James S., Reid, Gavin E., Moritz, Robert L., Simpson, Richard J.

“…The high affinity interleukin-6 (IL-6) receptor is a hexameric complex consisting of two molecules each of IL-6, IL-6 receptor (IL-6R), and the high affinity…”
Get full text

Fabrication of stable packed capillary reversed-phase columns for protein structural analysis by Tong, D, Moritz, R L, Eddes, J S, Reid, G E, Rasmussen, R K, Dorow, D S, Simpson, R J

“…Capillary column (< or = 320-micron ID) liquid chromatography is an essential tool for the separation and concentration of low-picomole amounts of proteins and…”
Get full text

Internal calibrants allow high accuracy peptide matching between MALDI imaging MS and LC-MS/MS: Imaging Mass Spectrometry: A User's Guide to a New Technique for Biological and Biomedical Research by GUSTAFSSON, Johan O. R, EDDES, James S, MEDING, Stephan, KOUDELKA, Tomas, OEHLER, Martin K, MCCOLL, Shaun R, HOFFMANN, Peter

Get full text