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Top-Down Proteomics: Ready for Prime Time?

Bifan Chen, Kyle A. Brown, Ziqing Lin, Ying Ge
2017 Analytical Chemistry  
Thus, signal suppression from salt adducts (i.e. Na + , K + ), detergents, or even coexisting protein species can greatly hamper a top-down experiment.  ...  The major functions of MASH Suite Pro include protein identification, quantitation, and characterization of protein PTMs from top-down MS and MS/MS experiments.  ...  (A) Representative mass spectra of RLC from 6, 24, and 36 month old rats.  ... 
doi:10.1021/acs.analchem.7b04747 pmid:29161012 pmcid:PMC6138622 fatcat:gq2bxvzsojgwbdvvmll7inhwb4

Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis

Samuel H. Payne, Margaret Yau, Marcus B. Smolka, Stephen Tanner, Huilin Zhou, Vineet Bafna
2008 Journal of Proteome Research  
In addition to being accurate, MS/MS identification software must be robust and efficient to deal with increasingly large spectral data sets.  ...  The scoring function was modeled by learning fragmentation patterns from 7677 validated phosphopeptide spectra. We compare our algorithm against SEQUEST and X!  ...  Generating the Training Set A total of 62 000 LTQ MS/MS spectra were generated from Saccharomyces cerevisiae and an additional 109 000 LTQ MS/MS spectra were generated from Schizosaccharomyces pombe.  ... 
doi:10.1021/pr800129m pmid:18563926 pmcid:PMC2566938 fatcat:y2dw3qw6kvd3fksg6bo4dz435m

A Systematic Statistical Analysis of Ion Trap Tandem Mass Spectra in View of Peptide Scoring [chapter]

Jacques Colinge, Alexandre Masselot, Jérôme Magnin
2003 Lecture Notes in Computer Science  
By using a huge collection of 140 000+ peptide MS/MS spectra, we systematically study the importance of many characteristics of a match (peptide sequence/spectrum) to include in a score function.  ...  In particular, it is of prime importance to design sensitive and selective score functions to reliably identify peptides in databases.  ...  MS/MS database searching usually involves the comparison of the experimental MS/MS spectrum with theoretical MS/MS spectra, computed from the peptide sequences found in the database.  ... 
doi:10.1007/978-3-540-39763-2_3 fatcat:ynkdam6usvhfdlxturwtqudlpq

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS

Yangyang Bian, Runsheng Zheng, Florian P. Bayer, Cassandra Wong, Yun-Chien Chang, Chen Meng, Daniel P. Zolg, Maria Reinecke, Jana Zecha, Svenja Wiechmann, Stephanie Heinzlmeir, Johannes Scherr (+5 others)
2020 Nature Communications  
Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC-MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness.  ...  CV) using data from >2000 samples of human cell lines, tissues and body fluids.  ...  Robustness and reproducibility of micro-flow LC-MS/MS.  ... 
doi:10.1038/s41467-019-13973-x pmid:31919466 pmcid:PMC6952431 fatcat:aix7c5u27ndb7deadzptgmo5qi

Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra

Niels Hulstaert, Florian Reisinger, Jonathan Rameseder, Harald Barsnes, Juan Antonio Vizcaíno, Lennart Martens
2013 Journal of Proteomics  
Pride-asap binaries, source code and additional information can be downloaded from  ...  We present an open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database.  ...  [12] , pride-asap does not seek to provide the most exhaustive possible annotation for a specific type of high mass accuracy MS/MS spectra, but rather focuses on a rigorous and robust annotation that  ... 
doi:10.1016/j.jprot.2013.04.011 pmid:23603108 pmcid:PMC4085470 fatcat:myaryyoiiraihnsxiglij7joyu

A graph-theoretic approach for the separation of b and y ions in tandem mass spectra

B. Yan, C. Pan, V. N. Olman, R. L. Hettich, Y. Xu
2004 Bioinformatics  
Results: Here, we present a novel graph-theoretic approach for solving the problem of separating b ions from y ions in a set of tandem mass spectra.  ...  We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME (PaRtition of Ion types in tandem Mass spEctra).  ...  .: From Molecular Machines to Hierarchical Modeling' (  ... 
doi:10.1093/bioinformatics/bti044 pmid:15454408 fatcat:ulsfhpsee5cozfaephi6k5oipe

Sequential primed kinases create a damage-responsive phosphodegron on Eco1

Nicholas A Lyons, Bryan R Fonslow, Jolene K Diedrich, John R Yates, David O Morgan
2013 Nature Structural & Molecular Biology  
These kinases recognize motifs primed by previous phosphorylation, resulting in an ordered sequence of three phosphorylation events on Eco1.  ...  This elaborate regulatory system, involving three independent kinases and stringent substrate selection by a ubiquitin ligase, enables robust control of cohesion establishment during normal growth and  ...  Datadependent acquisitions of MS/MS spectra with the LTQ on the Orbitrap XL were performed with the following settings: MS/MS on the eight most intense ions per precursor scan, 30K automatic gain control  ... 
doi:10.1038/nsmb.2478 pmid:23314252 pmcid:PMC3565030 fatcat:7jlyv5xszvg5ta6uczyord46jy

Automatic Quality Assessment of Peptide Tandem Mass Spectra

M. Bern, D. Goldberg, W. H. McDonald, J. R. Yates
2004 Bioinformatics  
Hence a filter that eliminates poor spectra before the database search can significantly improve throughput and robustness.  ...  Statistical regression can pick out spectra of modified peptides that can be identified by a de novo program but not by SEQUEST.  ...  peptide from bovine serum albumin.  ... 
doi:10.1093/bioinformatics/bth947 pmid:15262780 fatcat:6c3wndnsm5anbevercjxseps2y

MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis

Hiroshi Tsugawa, Tomas Cajka, Tobias Kind, Yan Ma, Brendan Higgins, Kazutaka Ikeda, Mitsuhiro Kanazawa, Jean VanderGheynst, Oliver Fiehn, Masanori Arita
2015 Nature Methods  
For reversed phase LC-MS/MS, our program with an enriched LipidBlast library identified total 1,023 lipid compounds from nine algal strains to highlight their chemotaxonomic relationships.  ...  Here we provide an open-source software pipeline, MS-DIAL, to demonstrate how DIA improves simultaneous identification and quantification of small molecules by mass spectral deconvolution.  ...  It will also benefit the proteomics community, where true mass spectral deconvolution has not been commonly utilized for peptide identifications.  ... 
doi:10.1038/nmeth.3393 pmid:25938372 pmcid:PMC4449330 fatcat:shxo3x5z3rbivblf37iwkbcuua

Peptidases released by necrotic cells control CD8+ T cell cross-priming

Jaba Gamrekelashvili, Tamar Kapanadze, Miaojun Han, Josef Wissing, Chi Ma, Lothar Jaensch, Michael P. Manns, Todd Armstrong, Elizabeth Jaffee, Ayla O. White, Deborah E. Citrin, Firouzeh Korangy (+1 others)
2013 Journal of Clinical Investigation  
Cross-priming of CD8 + T cells and generation of effector immune responses is pivotal for tumor immunity as well as for successful anticancer vaccination and therapy.  ...  We used a mouse model of sterile necrosis, in which mice were injected with sterile primary necrotic cells, to investigate a role of these cells in priming of CD8 + T cells.  ...  Scaffold (version Scaffold_3_00_03; Proteome Software Inc.) was used to validate MS/MS-based peptide and protein identifications.  ... 
doi:10.1172/jci65698 pmid:24216478 pmcid:PMC3809774 fatcat:qql2purfargbnh4mjigtu35rfq

After another decade: LC-MS/MS became routine in clinical diagnostics

Christoph Seger, Linda Salzmann
2020 Clinical Biochemistry  
The tasks that remain to be mastered are, for example, the quantification of proteins by means of LC-MS/MS and the transition from targeted to untargeted omics approaches relying on pattern recognition  ...  /MS instruments as an analytical core.  ...  The analytical readout -MS/MS spectra and retention times under controlled chromatographic conditions -was interpreted by comparison with model spectra from a database to allow (unequivocal) analyte assignment  ... 
doi:10.1016/j.clinbiochem.2020.03.004 pmid:32188572 fatcat:shxgfmrk5fgkjinkzsbqc5fmte

Rat Mammary Extracellular Matrix Composition and Response to Ibuprofen Treatment During Postpartum Involution by Differential GeLC–MS/MS Analysis

Jenean H. O'Brien, Lauren A. Vanderlinden, Pepper J. Schedin, Kirk C. Hansen
2012 Journal of Proteome Research  
GeLC-MS/MS experiments resulted in 20,327 peptide identifications that mapped to 884 proteins with a <0.02% false discovery rate.  ...  Previous studies show pro-tumorigenic properties of extracellular matrix (ECM) isolated from rodent mammary glands undergoing postpartum involution.  ...  Extracellular matrix protein identifications from our samples account for the highest number of peptide identifications as well as integrated peptide peak area (Fig. 3) .  ... 
doi:10.1021/pr3003744 pmid:22897585 pmcid:PMC4292908 fatcat:sisyus6vdjbtjaiotnmfrm3qbu

A mosquito lipoxin/lipocalin complex mediates innate immune priming in Anopheles gambiae

Jose Luis Ramirez, Giselle de Almeida Oliveira, Eric Calvo, Jesmond Dalli, Romain A. Colas, Charles N. Serhan, Jose M. Ribeiro, Carolina Barillas-Mury
2015 Nature Communications  
Plasmodium ookinete midgut invasion triggers immune priming by inducing the release of a mosquito lipoxin/ lipocalin complex.  ...  Challenged mosquitoes constitutively release a soluble haemocyte differentiation factor into their haemolymph that, when transferred into Naive mosquitoes, also induces priming.  ...  MS/MS fragmentation spectrum employed for the identification of (e) d 8 -LXA 4 and (f) d 8 -LXB 4 . Results for b-f are representative of two independent haemolymph preparations.  ... 
doi:10.1038/ncomms8403 pmid:26100162 pmcid:PMC4542143 fatcat:fispnq4cevhexearhlkbqgykgm

Proteomic Analyses Reveal an Acidic Prime Side Specificity for the Astacin Metalloprotease Family Reflected by Physiological Substrates

Christoph Becker-Pauly, Olivier Barré, Oliver Schilling, Ulrich auf dem Keller, Anke Ohler, Claudia Broder, André Schütte, Reinhild Kappelhoff, Walter Stöcker, Christopher M. Overall
2011 Molecular & Cellular Proteomics  
Such broad coverage enables family-wide determination of specificities N-and C-terminal to the scissile peptide bond.  ...  Using PICS (proteomic identification of protease cleavage site specificity) and TAILS (terminal amine isotopic labeling of substrates) degradomics approaches >3000 cleavage sites were proteomically identified  ...  These unprotected N-terminal ␣-amines at the prime-side of the cleavage products are selectively biotinylated to enable affinity isolation and LC-MS/MS based sequence identification.  ... 
doi:10.1074/mcp.m111.009233 pmid:21693781 pmcid:PMC3186203 fatcat:jzzni2k3fjhffj3335hzff22ne

Development and validation of an LC-MS/MS method for detection and quantification of in vivo derived metabolites of [Pyr1]apelin-13 in humans

Duuamene Nyimanu, Richard G. Kay, Petra Sulentic, Rhoda E. Kuc, Philip Ambery, Lutz Jermutus, Frank Reimann, Fiona M. Gribble, Joseph Cheriyan, Janet J. Maguire, Anthony P. Davenport
2019 Scientific Reports  
Plasma was extracted in the presence of guanidine hydrochloride and analysed by LC-MS/MS.  ...  Here we report a highly sensitive, robust and reproducible method for quantification of intact [Pyr1]apelin-13 and its metabolites in human plasma.  ...  Plasma samples from six individuals were also extracted to assess the selectivity of the LC-MS/MS method. Peptide Identification using high-resolution mass spectrometry.  ... 
doi:10.1038/s41598-019-56157-9 pmid:31882594 pmcid:PMC6934825 fatcat:yhxygftdajb33luxn34dtsp27a
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