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Highly sensitive feature detection for high resolution LC/MS

Ralf Tautenhahn, Christoph Bottcher, Steffen Neumann
2008 BMC Bioinformatics  
Results: We developed a new feature detection algorithm centWave for high-resolution LC/MS data sets, which collects regions of interest (partial mass traces) in the raw-data, and applies continuous wavelet  ...  Determining the boundaries, centres and intensities of the two-dimensional signals in the LC/MS raw data is called feature detection.  ...  Acknowledgements Thanks to Colin Smith, who started the Bioconductor package XCMS and to Pan Du who wrote the MassSpecWavelet package for some of the CWT code.  ... 
doi:10.1186/1471-2105-9-504 pmid:19040729 pmcid:PMC2639432 fatcat:wrast77hhrc2vei4wkoup77dou

LC/MS applications in drug development

Mike S. Lee, Edward H. Kerns
1999 Mass spectrometry reviews (Print)  
In this LC/MS application, the negative ion mode is highly sensitive for this class of compound.  ...  This analysis features a reduced resolution on both mass analyzers (Q1 and Q3) to obtain maximum sensitivity.  ...  ., LC/LC/MS/MS, LC/MS n ). The integration of expanded capabilities to increase performance will continue to impact chromatography and mass spectrometry formats.  ... 
doi:10.1002/(sici)1098-2787(1999)18:3/4<187::aid-mas2>;2-k pmid:10568041 fatcat:cpfuosdkpjh37hu26ixfhtmpsy

apLCMS—adaptive processing of high-resolution LC/MS data

Tianwei Yu, Youngja Park, Jennifer M. Johnson, Dean P. Jones
2009 Computer applications in the biosciences : CABIOS  
Result: Here we present a set of algorithms for the processing of high-resolution LC/MS data.  ...  Significant challenges exist in the analysis of LC/MS data, including noise reduction, feature identification/ quantification, feature alignment and computation efficiency.  ...  ACKNOWLEDGEMENTS The author thanks Dr Brani Vidakovic for helpful discussions, and three anonymous referees for valuable comments.  ... 
doi:10.1093/bioinformatics/btp291 pmid:19414529 pmcid:PMC2712336 fatcat:43qwnnga4bgoja5vmhtyfcvjfa

Isotopic labeling-assisted metabolomics using LC–MS

C. Bueschl, R. Krska, B. Kluger, R. Schuhmacher
2012 Analytical and Bioanalytical Chemistry  
This includes recognition of true metabolite-derived analytical features in highly complex LC-MS data and characterization of the global biochemical composition of biological samples.  ...  The analysis of mixtures of in-vivo-stable isotopic-labeled samples or reference substances with un-labeled samples leads to specific LC-MS data patterns which can be systematically exploited in practically  ...  Acknowledgments The authors thank the Austrian Science Fund (project SFB Fusarium 3706-B11) and the WWTF (project Toxi-Genome 9793008037) for financial support.  ... 
doi:10.1007/s00216-012-6375-y pmid:23010843 pmcid:PMC3536965 fatcat:fix6ev3ikrgfzeq77azzsvjqda

Comparative LC-MS: A landscape of peaks and valleys

Antoine H. P. America, Jan H. G. Cordewener
2008 Proteomics  
In order to compare at comprehensive scale peak intensity data in multiple LC-MS datasets, dedicated software is required for detection, matching and alignment of peaks.  ...  More recently, high resolution quantitative approaches are reported that rely on LC-MS quantitation of peptide concentrations by comparing peak intensities between multiple runs obtained by continuous  ...  While using the high resolution feature detection algorithms developed for comparative LC-MS the quantitative accuracy will improve even more, with this high density reference points.  ... 
doi:10.1002/pmic.200700694 pmid:18297651 fatcat:kdlh4bq2mjfufhdyygve23kzpe

Current Developments in LC-MS for Pharmaceutical Analysis

Chang-Kee Lim, Gwyn Lord
2002 Biological and Pharmaceutical Bulletin  
Liquid chromatography-mass spectrometry (LC-MS) is an analytical technique that couples high resolution chromatographic separation with sensitive and specific mass spectrometric detection.  ...  Various LC-MS techniques will be described briefly and the advantages and disadvantages of each will be discussed. DEVELOPMENTS IN LC-MS  ...  LC/MS has been the most prominent technique, with its high sensitivity and specificity.  ... 
doi:10.1248/bpb.25.547 pmid:12033491 fatcat:buhr2io3kvhtzklzutqn4erore

Neuroproteomics — LC-MS Quantitative Approaches [chapter]

Cátia Santa, Sandra I. Anjo, Vera M. Mendes, Bruno Manadas
2015 Recent Advances in Proteomics Research  
For this, mass spectrometry approaches, most often coupled with liquid chromatography (LC-MS), have been the number one choice in proteomics, and over the years it has added many important findings to  ...  Therefore, many LC-MS quantitative approaches have been developed relying on the labeling of the proteins or even by using label-free techniques.  ...  LC-MS E : Silva and colleagues reported in 2006 Three most intense peptides peak area (T3PQ): The T3PQ method is an adaptation of the method previously used in LC-MS E [177] for IDA methods [157] .  ... 
doi:10.5772/61298 fatcat:3lfioog2kzerxmyra5koo7vgha

A Review: Protein Identification by LC-MS: Principles, Instrumentation, and Applications

Abeer Salh Alhendi
2020 Iraqi Journal of Science  
Characterization of proteins provides a foundation for the fundamental understanding of biology aspects.  ...  High-performance liquid chromatography (HPLC) is an important technique that is usually applied before MS is conducted due to its efficient separation.  ...  Acknowledgments The author is thankful to the Associate Professor Nicole Horenstein for her help with this reviewing article .  ... 
doi:10.24996/ijs.2020.61.10.2 fatcat:aoucrzplgjac5m7kynzuadayfy


2017 Malaysian Journal of Analytical Science  
resolution mass spectrometer (LC-MS) after labelling them to improve MS ionization.  ...  Multivariate analysis showed distinct clustering of samples belonging to each bacterial species and revealed certain features that can be potential species and serotype-specific markers of LPS from the  ...  Nur Wahdiah Binte Mohamed Safit for the help with the Malay translations.  ... 
doi:10.17576/mjas-2017-2106-18 fatcat:xifgyx6re5hslbdaj4tcyscc2m

LC–MS Based Detection of Differential Protein Expression

Leepika Tuli, Habtom W. Ressom
2009 Journal of Proteomics & Bioinformatics  
While several techniques are available in proteomics, LC-MS based analysis of complex protein/peptide mixtures has turned out to be a mainstream analytical technique for quantitative proteomics.  ...  Moreover, automation and robotics for sample handling process permit multiple sampling with high throughput.  ...  Acknowledgements This work was supported in part by the National Science Foundation Grant IIS-0812246, the National Cancer Institute (NCI) R21CA130837 Grant, NCI Early Detection Research Network Associate  ... 
doi:10.4172/jpb.1000102 pmid:20473349 pmcid:PMC2867618 fatcat:weyv7yegwjhlnotanbmsm7fjca

Multianalyte LC–MS-based methods in doping control: what are the implications for doping athletes?

Francesco Botrè, Xavier de la Torre, Monica Mazzarino
2016 Bioanalysis  
To also detect potentially unknown targets, high-resolution mass spectrometers operating in fullscan mode can be used for the detection of a virtually unlimited range of known and unknown substances.  ...  A peculiar feature of the newly developed LC-MS(/MS)-based procedures was the possibility to screen for a considerable number of markedly different analytes/classes of analytes in a single chromatographic  ... 
doi:10.4155/bio-2016-0083 pmid:27212276 fatcat:xhvabd3u3nhytfubag4gxj2cg4

Analytical strategies for LC–MS-based targeted metabolomics

Wenyun Lu, Bryson D. Bennett, Joshua D. Rabinowitz
2008 Journal of chromatography. B  
Applicability to targeted metabolomics of triple quadrupole mass spectrometry operating in multiple reaction monitoring (MRM) mode and high mass resolution full scan mass spectrometry (e.g., time-of-flight  ...  Here we discuss several issues relevant to developing liquid chromatography-electrospray ionization-mass spectrometry methods for targeted metabolomics (i.e., quantitative analysis of dozens to hundreds  ...  Ferguson from AppliedBiosystems for analyses of selected samples, and Mark Sanders and the reviewers for comments on the manuscript.  ... 
doi:10.1016/j.jchromb.2008.04.031 pmid:18502704 pmcid:PMC2607197 fatcat:4ihm4gto5nfazkve7w2c6ucg7m

Highly Sensitive Determination of Amino Acids by LC-MS under Neutral Conditions

Ryota Morimoto, Takumi Matsumoto, Mayuri Minote, Masayuki Yanagisawa, Ryotaro Yamada, Takefumi Kuranaga, Hideaki Kakeya
2021 Chemical and pharmaceutical bulletin  
Herein, we firstly report the improved LC-MS protocols for the highly sensitive analyses of amino acids.  ...  In an LC-MS-based structural study of peptides, these reagents enabled us to detect infinitesimal amounts of amino acids derived from mild degradative analysis of the samples.  ...  If the labeled amino acids can be detected at high sensitivity under neutral conditions, costly LC-MS-grade acidic additives would not be required.  ... 
doi:10.1248/cpb.c20-00958 pmid:33642474 fatcat:pqqbji6oazefbdoh7p6tvl4fhm

Acylcarnitine profiling by low-resolution LC-MS

David Meierhofer, Francisco J. Schopfer
2019 PLoS ONE  
Altogether 123 acylcarnitines species were used to establish a targeted low-resolution LC-MS method.  ...  Therefore, a method for the simultaneous fast and robust detection of all known acylcarnitines was developed using a single concise liquid chromatography mass spectrometry (LC-MS) approach.  ...  Acknowledgments The author is grateful to Beata Lukaszewska-McGreal for technical assistance and to Corinna Schwichtenberg for mouse tissue dissection. Author Contributions  ... 
doi:10.1371/journal.pone.0221342 pmid:31415665 pmcid:PMC6695155 fatcat:wibmz2wk6jc6hjcnfshd7f3yzm

Lipid Discovery by Combinatorial Screening and Untargeted LC-MS/MS

Mesut Bilgin, Petra Born, Filomena Fezza, Michael Heimes, Nicolina Mastrangelo, Nicolai Wagner, Carsten Schultz, Mauro Maccarrone, Suzanne Eaton, André Nadler, Matthias Wilm, Andrej Shevchenko
2016 Scientific Reports  
Instead, all precursors co-eluted during LC-MS/MS experiment may be fragmented at once and all fragments simultaneously detected in a highly convoluted spectrum -this approach was termed as MS E and also  ...  as all-ions fragmentation LC-MS/MS (AIF LC-MS/MS) 7-10 .  ...  Software for AIF LC-MS/MS discovery screening. AIF LC-MS/MS spectra were processed by Arcadiate 2.0 software, a tool for visualization and analysis of LC-MS/MS data.  ... 
doi:10.1038/srep27920 pmid:27312775 pmcid:PMC4911551 fatcat:fwljay7v65bg3l2clpmi4vw3pa
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