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Christian Schley, Matthias Altmeyer, Rolf Müller, Christian G. Huber, Oliver Kohlbacher, Knut Reinert
In order to generate proteomics data that are suitable to validate protein identification in complex mixtures using multidimensional liquid-chromatography-mass spectrometry approaches, we implemented an  ...  The fragment ion spectra generated by ESI-MS/MS were subsequently analyzed via MASCOT database search.  ...  with the obtained identification data from Mascot database search.  ... 
doi:10.4230/dagsemproc.05471.11 fatcat:szl2t3elnrhdvbwwbgwzobpoo4

Off-Line Multidimensional Liquid Chromatography and Auto Sampling Result in Sample Loss in LC/LC–MS/MS

Sameh Magdeldin, James J. Moresco, Tadashi Yamamoto, John R. Yates
2014 Journal of Proteome Research  
Our findings revealed that online MudPIT provided more peptide/protein identifications and higher sequence coverage than offline platforms.  ...  In this study, we evaluated the performance of different MudPIT strategies by both label-free and tandem mass tag (TMT) isobaric tagging.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.1021/pr500530e pmid:25040086 pmcid:PMC4123945 fatcat:sewvxzxwsbflvcjgvn37ybrqia

Defining the Neuropeptidome of the Spiny Lobster Panulirus interruptus Brain Using a Multidimensional Mass Spectrometry-Based Platform

Hui Ye, Jingxin Wang, Zichuan Zhang, Chenxi Jia, Claire Schmerberg, Adam D. Catherman, Paul M. Thomas, Neil L. Kelleher, Lingjun Li
2015 Journal of Proteome Research  
Our streamlined process searched the high mass accuracy and highresolution data acquired on a LTQ-Orbitrap with a flexible algorithm in ProSight that allows for sequence discrepancy from reported sequences  ...  By taking advantage of sequence homology in neuropeptides observed in related species using a home-built crustacean neuropeptide database, we developed a semi-automated sequencing strategy to characterize  ...  This work is supported in part by the National Institutes of Health grants (R01DK071801 and 1S10RR029531 to LL) and the National Science  ... 
doi:10.1021/acs.jproteome.5b00627 pmid:26390183 pmcid:PMC4654452 fatcat:nwwqjs732rdknjhyxjk2vwbevm

Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling

Jaeho Paek, Marian Kalocsay, Dean P. Staus, Laura Wingler, Roberta Pascolutti, Joao A. Paulo, Steven P. Gygi, Andrew C. Kruse
2017 Cell  
Combination of this technique with isobaric labeling and triple-stage mass spectrometry enables precise, quantitative, and timeresolved measurement of thousands of receptor-proximal proteins at their native  ...  Using this technique, we examine the response of the angiotensin II type 1 receptor to both balanced and biased agonists.  ...  Funding was provided by the Smith Family Foundation (A.C.K), the Vallee Foundation (A.C.K.), the Esther A. and Joseph Klingenstein Fund (A.C.K.), Biogen Idec (S.P.G.) and NIH grants R01HL016037 and 1DP5OD021345  ... 
doi:10.1016/j.cell.2017.03.028 pmid:28388415 pmcid:PMC5514552 fatcat:xpiv7wcrerdyjazl5wt4bt5kq4

Proteomics of the Eukaryotic Transcription Machinery: Identification of Proteins Associated with Components of Yeast TFIID by Multidimensional Mass Spectrometry

S. L. Sanders, J. Jennings, A. Canutescu, A. J. Link, P. A. Weil
2002 Molecular and Cellular Biology  
coupled multidimensional liquid chromatography and tandem mass spectrometry.  ...  Toward this end, TFIID was systematically immunopurified by using polyclonal antibodies directed against each subunit, and the constellation of TBP-and TAF-associated proteins was directly identified by  ...  This work was supported by National Institutes of Health Grant GM52461 (P.A.W.) and by Vanderbilt-Ingram Cancer Support grant 5P30CA68485, HHMI, and Ingram Family gift (A.J.L.).  ... 
doi:10.1128/mcb.22.13.4723-4738.2002 pmid:12052880 pmcid:PMC133885 fatcat:lgrdxiy4yjaopj67476bb7lf64

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

Jens Allmer, Sebastian Kuhlgert, Michael Hippler
2008 BMC Bioinformatics  
A novel feature and a focus of this database is to facilitate protein identification by using peptides identified from mass spectrometry and link this information directly to respective protein maps.  ...  Conclusion: We present a proteomics database which aims to greatly reduce evaluation time of results from mass spectrometric experiments and enhance result quality by allowing consistent data handling.  ...  Acknowledgements We would like to thank Simon Mumford who edited the final version of this publication and Rainer Perske who promptly fixed all problems in our database and web development environment.  ... 
doi:10.1186/1471-2105-9-302 pmid:18605993 pmcid:PMC2475538 fatcat:s6evcr4omjburoweqxv5bvbarm

High-throughput proteomics using matrix-assisted laser desorption/ ionization mass spectrometry

Rainer Cramer, Johan Gobom, Eckhard Nordhoff
2005 Espert Review of Proteomics  
. • For optimal data exploitation and high-throughput proteomics, it is essential to develop advanced bioinformatic tools for data management and analysis.  ...  This review will provide some basics, thoughts and ideas on the exploitation of matrix-assisted laser desorption/ ionization in biological mass spectrometry -one of the most commonly used analytical tools  ...  In a database search, these mass values are matched against sets of proteolytic peptide masses calculated for all protein sequences in a sequence database.  ... 
doi:10.1586/14789450.2.3.407 pmid:16000086 fatcat:b7j2hophrvbazntaftghwbgxua

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field

Emmalyn J. Dupree, Madhuri Jayathirtha, Hannah Yorkey, Marius Mihasan, Brindusa Alina Petre, Costel C. Darie
2020 Proteomes  
Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls.  ...  Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one.  ...  Acknowledgments: We thank the past and current members of the Biochemistry & Proteomics Group for the pleasant working environment.  ... 
doi:10.3390/proteomes8030014 pmid:32640657 pmcid:PMC7564415 fatcat:w3gv37fcynfqxpvjsyroutryum

Immobilized pH gradient isoelectric focusing as a first-dimension separation in shotgun proteomics

Benjamin J Cargile, Joel R Sevinsky, Amal S Essader, James L Stephenson, Jonathan L Bundy
2005 Journal of Biomolecular Techniques  
prospects for the use of peptide pI along with accurate mass measurement for the identification of peptides.  ...  Shotgun proteomics, where a tryptic digest of a complex proteome sample is directly analyzed by either single dimensional or multidimensional liquid chromatography tandem mass spectrometry, has gained  ...  Financial support for research performed in our laboratories was provided by Internal Research and Development funds from RTI and an unrestricted grant from Merck and Co.  ... 
pmid:16461941 pmcid:PMC2291737 fatcat:ln557md25bgohga5tjwodyvxf4

Inference and Validation of Protein Identifications

Manfred Claassen
2012 Molecular & Cellular Proteomics  
The inherent uncertainty of mass spectrometric data and the complexity of a proteome render protein inference and the statistical validation of protein identifications a non-trivial task, still being a  ...  Reconstruction of protein identities from the raw mass spectrometric data constitutes a cornerstone of any shotgun proteomics workflow.  ...  Spectral alignment approaches take a special position and start off from the raw mass spectrometrical data and de novo assemble (partial) protein sequences by aligning fragment ion spectra of overlapping  ... 
doi:10.1074/mcp.r111.014795 pmid:22865921 pmcid:PMC3494198 fatcat:jesgfw5ytvgafg2ndogtsbxxpi

Managing Proteomics Data: From Generation and Data Warehousing to Central Data Repository

Herbert Thiele, Jorg Glandorf, Peter Hufnagel, Gerhard Korting, Martin Bluggel
2008 Journal of Proteomics & Bioinformatics  
, the use of Decoy databases to measure the false positive rate (FPR), the combination of peptide results by the ProteinExtractor algorithm to non-redundant protein lists with known FPR, the automatic  ...  As a specific example of the HUPO based data processing strategy, the analysis of a large proteomics data set is described, including the automatic search over four search engines to generate peptide results  ...  analytical methods to identify peptides, proteins and their post translational modifications, e.g with mass spectrometry.  ... 
doi:10.4172/jpb.1000056 fatcat:dsa3gzfj3ndmvbpqc4lme64v64

Managing Proteomics Data from Generation and Data Warehousing to Central Data Repository

H. Thiele, J. Glandorf, P. Hufnagel
2008 Journal of Proteomics & Bioinformatics  
, the use of Decoy databases to measure the false positive rate (FPR), the combination of peptide results by the ProteinExtractor algorithm to non-redundant protein lists with known FPR, the automatic  ...  As a specific example of the HUPO based data processing strategy, the analysis of a large proteomics data set is described, including the automatic search over four search engines to generate peptide results  ...  analytical methods to identify peptides, proteins and their post translational modifications, e.g with mass spectrometry.  ... 
doi:10.4172/jpb.s1000030 fatcat:kr34d5wjlzfnhec4u5f4ebe4hy

A Smart Way for Talking With Proteins; Proteomics

Ömür Baysal
2017 MOJ Proteomics & Bioinformatics  
By using the high throughput mass spectrometer technology, huge output data of peptide spectra has been generated.  ...  roles of proteins following protein isolation, digestion and mass spectrometry.  ...  PRIDE [52] has peptide/protein identifications including PTMs, expression values, the analyzed mass spectra, and the related metadata.  ... 
doi:10.15406/mojpb.2017.05.00160 fatcat:wpcogwvbivgdvez5p5a2ordgjq

Managing of Unassigned Mass Spectrometric Data by Neural Network for Cancer Phenotypes Classification

Denis V. Petrovsky, Arthur T. Kopylov, Vladimir R. Rudnev, Alexander A. Stepanov, Liudmila I. Kulikova, Kristina A. Malsagova, Anna L. Kaysheva
2021 Journal of Personalized Medicine  
The development of machine learning methods for the intelligent analysis of raw mass spectrometric (HPLC-MS/MS) measurements without involving the stages of preprocessing and data identification seems  ...  Mass spectrometric profiling provides information on the protein and metabolic composition of biological samples.  ...  Acknowledgments: Mass spectrometric measurements were performed using the equipment of the "Human Proteome" Core Facility (IBMC, Moscow, Russia).  ... 
doi:10.3390/jpm11121288 pmid:34945760 pmcid:PMC8707435 fatcat:bne4mdol5fhjxmvymt6ycybuki

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective

Yasset Perez-Riverol, Rui Wang, Henning Hermjakob, Markus Müller, Vladimir Vesada, Juan Antonio Vizcaíno
2014 Biochimica et Biophysica Acta - Proteins and Proteomics  
From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features  ...  Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including  ...  Table 2 shows different libraries that can be used to read and write MS files formats (both peak list and peptide/protein identification files).  ... 
doi:10.1016/j.bbapap.2013.02.032 pmid:23467006 pmcid:PMC3898926 fatcat:ush24sgygvc2jbmlgeyf4xg7hi
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