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  1. Article ; Online: Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.

    Eng, Jimmy K / Deutsch, Eric W

    Proteomics

    2020  Volume 20, Issue 21-22, Page(s) e1900362

    Abstract: Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is ... ...

    Abstract Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard for the representation of sequence databases used as input to sequence database search tools is the FASTA format. The Human Proteome Organization's Proteomics Standards Initiative has developed an extension to the FASTA format termed the proteomics standards initiative extended FASTA format or PSI extended FASTA format (PEFF) where additional information such as structural annotations are encoded in the protein description lines. Comet has been extended to automatically analyze the post translational modifications and amino acid substitutions encoded in PEFF databases. Comet's PEFF implementation and example analysis results searching a HEK293 dataset against the neXtProt PEFF database are presented.
    MeSH term(s) Amino Acids ; Databases, Protein ; HEK293 Cells ; Humans ; Protein Processing, Post-Translational ; Proteome ; Proteomics ; Software
    Chemical Substances Amino Acids ; Proteome
    Language English
    Publishing date 2020-04-02
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.201900362
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.

    Deutsch, Eric W / Mendoza, Luis / Shteynberg, David D / Hoopmann, Michael R / Sun, Zhi / Eng, Jimmy K / Moritz, Robert L

    Journal of proteome research

    2023  Volume 22, Issue 2, Page(s) 615–624

    Abstract: The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large ... ...

    Abstract The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has been in continual development and refinement since its first tools, PeptideProphet and ProteinProphet, were published 20 years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. Many of the tools include machine-learning modeling to extract the most information from data sets and build robust statistical models to compute the probabilities that derived information is correct. Here we present the latest information on the many TPP tools, and how TPP can be deployed on various platforms from personal Windows laptops to Linux clusters and expansive cloud computing environments. We describe tutorials on how to use TPP in a variety of ways and describe synergistic projects that leverage TPP. We conclude with plans for continued development of TPP.
    MeSH term(s) Proteomics/methods ; Software ; Mass Spectrometry ; Probability ; Data Analysis
    Language English
    Publishing date 2023-01-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00624
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  3. Article ; Online: The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.

    Kertesz-Farkas, Attila / Nii Adoquaye Acquaye, Frank Lawrence / Bhimani, Kishankumar / Eng, Jimmy K / Fondrie, William E / Grant, Charles / Hoopmann, Michael R / Lin, Andy / Lu, Yang Y / Moritz, Robert L / MacCoss, Michael J / Noble, William Stafford

    Journal of proteome research

    2023  Volume 22, Issue 2, Page(s) 561–569

    Abstract: The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive ... ...

    Abstract The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments since 2014. We begin with empirical results demonstrating our recently implemented speedups to the Tide search engine. Other new features include a new score function in Tide, two new confidence estimation procedures, as well as three new tools: Param-medic for estimating search parameters directly from mass spectrometry data, Kojak for searching cross-linked mass spectra, and DIAmeter for searching data independent acquisition data against a sequence database.
    MeSH term(s) Software ; Tandem Mass Spectrometry/methods ; Proteomics/methods ; Databases, Protein ; Algorithms
    Language English
    Publishing date 2023-01-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.2c00615
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  4. Article ; Online: Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification.

    Smith, Ian R / Eng, Jimmy K / Barente, Anthony S / Hogrebe, Alexander / Llovet, Ariadna / Rodriguez-Mias, Ricard A / Villén, Judit

    Analytical chemistry

    2022  Volume 94, Issue 44, Page(s) 15198–15206

    Abstract: Stable-isotope labeling with amino acids in cell culture (SILAC)-based metabolic labeling is a widely adopted proteomics approach that enables quantitative comparisons among a variety of experimental conditions. Despite its quantitative capacity, SILAC ... ...

    Abstract Stable-isotope labeling with amino acids in cell culture (SILAC)-based metabolic labeling is a widely adopted proteomics approach that enables quantitative comparisons among a variety of experimental conditions. Despite its quantitative capacity, SILAC experiments analyzed with data-dependent acquisition (DDA) do not fully leverage peptide pair information for identification and suffer from undersampling compared to label-free proteomic experiments. Herein, we developed a DDA strategy that coisolates and fragments SILAC peptide pairs and uses y-ions for their relative quantification. To facilitate the analysis of this type of data, we adapted the Comet sequence database search engine to make use of SILAC peptide paired fragments and developed a tool to annotate and quantify MS/MS spectra of coisolated SILAC pairs. This peptide pair coisolation approach generally improved expectation scores compared to the traditional DDA approach. Fragment ion quantification performed similarly well to precursor quantification in the MS1 and achieved more quantifications. Lastly, our method enables reliable MS/MS quantification of SILAC proteome mixtures with overlapping isotopic distributions. This study shows the feasibility of the coisolation approach. Coupling this approach with intelligent acquisition strategies has the potential to improve SILAC peptide sampling and quantification.
    MeSH term(s) Isotope Labeling/methods ; Peptide Fragments ; Peptides ; Proteome/analysis ; Proteomics/methods ; Tandem Mass Spectrometry/methods
    Chemical Substances Peptide Fragments ; Peptides ; Proteome
    Language English
    Publishing date 2022-10-28
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.2c01711
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  5. Article: Predictive proteomic signatures for response of pancreatic cancer patients receiving chemotherapy.

    Peng, Hong / Chen, Ru / Brentnall, Teresa A / Eng, Jimmy K / Picozzi, Vincent J / Pan, Sheng

    Clinical proteomics

    2019  Volume 16, Page(s) 31

    Abstract: ... proteins, including vitamin-K dependent protein Z (PZ), sex hormone-binding globulin (SHBG), von Willebrand ...

    Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is a lethal cancer that is characterized by its poor prognosis, rapid progression and development of drug resistance. Chemotherapy is a vital treatment option for most of PDAC patients. Stratification of PDAC patients, who would have a higher likelihood of responding to chemotherapy, could facilitate treatment selection and patient management.
    Methods: A quantitative proteomic study was performed to characterize the protein profiles in the plasma of PDAC patients undergoing chemotherapy to determine if specific biomarkers could be used to predict likelihood of therapeutic response.
    Results: By comparing the plasma proteome of the PDAC patients with positive therapeutic response and longer overall survival (Good-responders) to those who did not respond as well with shorter survival time (Limited-responders), we identified differential proteins and protein variants that could effectively segregate Good-responders from Limited-responders. Functional clustering and pathway analysis further suggested that many of these differential proteins were involved in pancreatic tumorigenesis. Four proteins, including vitamin-K dependent protein Z (PZ), sex hormone-binding globulin (SHBG), von Willebrand factor (VWF) and zinc-alpha-2-glycoprotein (AZGP1), were further evaluated as single or composite predictive biomarker with/without inclusion of CA 19-9. A composite biomarker panel that consists of PZ, SHBG, VWF and CA 19-9 demonstrated the best performance in distinguishing Good-responders from Limited-responders.
    Conclusion: Based on the cohort investigated, our data suggested that systemic proteome alterations involved in pathways associated with inflammation, immunoresponse, coagulation and complement cascades may be reporters of chemo-treatment outcome in PDAC patients. For the majority of the patients involved, the panel consisting of PZ, SHBG, VWF and CA 19-9 was able to segregate Good-responders from Limited-responders effectively. Our data also showed that dramatic fluctuations of biomarker concentration in the circulating system of a PDAC patient, which might result from biological heterogeneity or confounding complications, could diminish the performance of a biomarker. Categorization of PDAC patients in terms of their tumor stages and histological types could potentially facilitate patient stratification for treatment.
    Language English
    Publishing date 2019-07-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2205154-5
    ISSN 1542-6416
    ISSN 1542-6416
    DOI 10.1186/s12014-019-9251-3
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  6. Article ; Online: Tools for 3D Interactome Visualization.

    Keller, Andrew / Chavez, Juan D / Eng, Jimmy K / Thornton, Zorian / Bruce, James E

    Journal of proteome research

    2018  Volume 18, Issue 2, Page(s) 753–758

    Abstract: In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection ...

    Abstract In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL-MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL-MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. We have developed new informatics capabilities, the first to enable 3D visualization of multiple quantitative interactome data sets, acquired over time or with varied perturbation levels, to reveal relevant dynamic interactome changes. These new tools are integrated within release 3.0 of our online cross-linked peptide database and analysis tool suite XLinkDB. With the recent rapid expansion in XL-MS for protein structural studies and the extension to quantitative XL-MS measurements, 3D interactome visualization tools are of critical need.
    MeSH term(s) Computational Biology ; Humans ; Models, Molecular ; Protein Conformation ; Protein Interaction Mapping/methods ; Proteins/analysis ; Proteins/physiology ; Proteomics/methods ; Software
    Chemical Substances Proteins
    Language English
    Publishing date 2018-12-18
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.8b00703
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  7. Article ; Online: In Vivo Cross-Linking MS Reveals Conservation in OmpA Linkage to Different Classes of β-Lactamase Enzymes.

    Zhong, Xuefei / Wu, Xia / Schweppe, Devin K / Chavez, Juan D / Mathay, Martin / Eng, Jimmy K / Keller, Andrew / Bruce, James E

    Journal of the American Society for Mass Spectrometry

    2019  Volume 31, Issue 2, Page(s) 190–195

    Abstract: Molecular interactions between two different classes of β-lactamase enzymes and outer membrane protein A (OmpA) were studied by in vivo chemical cross-linking of a multi-drug-resistant strain ... ...

    Abstract Molecular interactions between two different classes of β-lactamase enzymes and outer membrane protein A (OmpA) were studied by in vivo chemical cross-linking of a multi-drug-resistant strain of
    MeSH term(s) Acinetobacter baumannii/chemistry ; Acinetobacter baumannii/metabolism ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/chemistry ; Bacterial Outer Membrane Proteins/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Conserved Sequence ; Cross-Linking Reagents/chemistry ; Mass Spectrometry ; Models, Molecular ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Interaction Maps ; beta-Lactamases/chemistry ; beta-Lactamases/metabolism
    Chemical Substances Bacterial Outer Membrane Proteins ; Bacterial Proteins ; Cross-Linking Reagents ; OMPA outer membrane proteins (149024-69-1) ; beta-Lactamases (EC 3.5.2.6)
    Language English
    Publishing date 2019-11-21
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1073671-2
    ISSN 1879-1123 ; 1044-0305
    ISSN (online) 1879-1123
    ISSN 1044-0305
    DOI 10.1021/jasms.9b00021
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  8. Article ; Online: Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification.

    Mohr, Jared P / Perumalla, Poorna / Chavez, Juan D / Eng, Jimmy K / Bruce, James E

    Analytical chemistry

    2018  Volume 90, Issue 10, Page(s) 6028–6034

    Abstract: Chemical cross-linking combined with mass spectrometry provides a method to study protein structures and interactions. The introduction of cleavable bonds in a cross-linker provides an avenue to decouple released peptide masses from their precursor ... ...

    Abstract Chemical cross-linking combined with mass spectrometry provides a method to study protein structures and interactions. The introduction of cleavable bonds in a cross-linker provides an avenue to decouple released peptide masses from their precursor species, greatly simplifying the downstream search, allowing for whole proteome investigations to be performed. Typically, these experiments have been challenging to carry out, often utilizing nonstandard methods to fully identify cross-linked peptides. Mango is an open source software tool that extracts precursor masses from chimeric spectra generated using cleavable cross-linkers, greatly simplifying the downstream search. As it is designed to work with chimeric spectra, Mango can be used on traditional high-resolution tandem mass spectrometry (MS/MS) capable mass spectrometers without the need for additional modifications. When paired with a traditional proteomics search engine, Mango can be used to identify several thousand cross-linked peptide pairs searching against the entire Escherichia coli proteome. Mango provides an avenue to perform whole proteome cross-linking experiments without specialized instrumentation or access to nonstandard methods.
    MeSH term(s) Cross-Linking Reagents/analysis ; Cross-Linking Reagents/pharmacology ; Escherichia coli/chemistry ; Mass Spectrometry ; Peptides/analysis ; Peptides/pharmacology ; Proteome/antagonists & inhibitors ; Proteome/metabolism ; Software
    Chemical Substances Cross-Linking Reagents ; Peptides ; Proteome
    Language English
    Publishing date 2018-04-27
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.7b04991
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: In Vivo Conformational Dynamics of Hsp90 and Its Interactors.

    Chavez, Juan D / Schweppe, Devin K / Eng, Jimmy K / Bruce, James E

    Cell chemical biology

    2016  Volume 23, Issue 6, Page(s) 716–726

    Abstract: Hsp90 belongs to a family of some of the most highly expressed heat shock proteins that function as molecular chaperones to protect the proteome not only from the heat shock but also from other misfolding events. As many client proteins of Hsp90 are ... ...

    Abstract Hsp90 belongs to a family of some of the most highly expressed heat shock proteins that function as molecular chaperones to protect the proteome not only from the heat shock but also from other misfolding events. As many client proteins of Hsp90 are involved in oncogenesis, this chaperone has been the focus of intense research efforts. Yet, we lack structural information for how Hsp90 interacts with co-chaperones and client proteins. Here, we developed a mass-spectrometry-based approach that allowed quantitative measurements of in vitro and in vivo effects of small-molecule inhibitors on Hsp90 conformation, and interaction with co-chaperones and client proteins. From this analysis, we were able to derive structural models for how Hsp90 engages its interaction partners in vivo, and how different drugs affect these structures. In addition, the methodology described here offers a new approach to probe the effects of virtually any inhibitor treatment on the proteome level.
    MeSH term(s) Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Chaperonins/chemistry ; Chaperonins/metabolism ; Eye Proteins/chemistry ; Eye Proteins/metabolism ; HSP70 Heat-Shock Proteins/chemistry ; HSP70 Heat-Shock Proteins/metabolism ; HSP90 Heat-Shock Proteins/antagonists & inhibitors ; HSP90 Heat-Shock Proteins/chemistry ; HSP90 Heat-Shock Proteins/metabolism ; HeLa Cells ; Heat-Shock Proteins/chemistry ; Heat-Shock Proteins/metabolism ; Humans ; Mass Spectrometry ; Models, Molecular ; Nerve Tissue Proteins/chemistry ; Nerve Tissue Proteins/metabolism ; Protein Binding ; Protein Conformation ; Small Molecule Libraries/pharmacology ; Tumor Cells, Cultured
    Chemical Substances CDC37 protein, human ; CHRDL1 protein, human ; Cell Cycle Proteins ; Eye Proteins ; HSP70 Heat-Shock Proteins ; HSP90 Heat-Shock Proteins ; Heat-Shock Proteins ; Nerve Tissue Proteins ; STIP1 protein, human ; Small Molecule Libraries ; Chaperonins (EC 3.6.1.-)
    Language English
    Publishing date 2016-10-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 2451-9448
    ISSN (online) 2451-9448
    DOI 10.1016/j.chembiol.2016.05.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: Tools for 3D Interactome Visualization

    Keller, Andrew / Chavez, Juan D / Eng, Jimmy K / Thornton, Zorian / Bruce, James E

    Journal of proteome research. 2018 Dec. 06, v. 18, no. 2

    2018  

    Abstract: In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL–MS) enable the detection ...

    Abstract In cells, intra- and intermolecular interactions of proteins confer function, and the dynamic modulation of this interactome is critical to meet the changing needs required to support life. Cross-linking and mass spectrometry (XL–MS) enable the detection of both intra- and intermolecular protein interactions in organelles, cells, tissues, and organs. Quantitative XL–MS enables the detection of interactome changes in cells due to environmental, phenotypic, pharmacological, or genetic perturbations. We have developed new informatics capabilities, the first to enable 3D visualization of multiple quantitative interactome data sets, acquired over time or with varied perturbation levels, to reveal relevant dynamic interactome changes. These new tools are integrated within release 3.0 of our online cross-linked peptide database and analysis tool suite XLinkDB. With the recent rapid expansion in XL–MS for protein structural studies and the extension to quantitative XL–MS measurements, 3D interactome visualization tools are of critical need.
    Keywords animal tissues ; chemical interactions ; crosslinking ; data collection ; databases ; mass spectrometry ; organelles ; phenotype ; proteins ; proteome
    Language English
    Dates of publication 2018-1206
    Size p. 753-758.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.8b00703
    Database NAL-Catalogue (AGRICOLA)

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