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A maximum-likelihood approach to absolute protein quantification in mass spectrometry
2015
Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics - BCB '15
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Label-free absolute protein quantification refers to a process of estimating protein abundances in complex biological samples based on the data acquired from a liquid chromatography mass spectrometry ( ...
In this work, we developed a new algorithm for absolute quantification of proteins. ...
This research was supported in part by Lilly Endowment, Inc., through its support for the Indiana University Pervasive Technology Institute, and in part by the Indiana METACyt Initiative. ...
doi:10.1145/2808719.2808750
dblp:conf/bcb/JiLBLART15
fatcat:oenafvfauncwxivkc2iu2gzita
On protein abundance distributions in complex mixtures
2013
Proteome Science
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Quantitative proteomic mass spectrometry on biological samples focuses on identifying the proteins present in the samples, and establishing the relative abundances of those proteins. ...
We have previously introduced a normalized, label-free method for quantification of protein abundances under a shotgun proteomics platform (Griffin et al., 2010) . ...
There are at present three principal methods of quantifying proteins via mass spectrometry: labeling approaches such as iTRAQ and SILAC, which aim to reduce experimental variance and allow relative comparison ...
doi:10.1186/1477-5956-11-5
pmid:23360617
pmcid:PMC3599228
fatcat:f7qf2sbbarfazgnvcmapubwngu
Bioinformatics Tools for Mass Spectrometry-Based High-Throughput Quantitative Proteomics Platforms
2011
Current Protoemics
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Liquid chromatography, coupled to mass spectrometry, has been widely used as a proteomics technique for discovering differentially expressed proteins in biological samples. ...
The use of different approaches to data processing and analyses is among the factors which contribute to inconsistent conclusions. ...
When peptide ratios were assembled into a protein ratio using maximum likelihood point estimation, it was shown that this approach is more accurate than averaging ratios [68] . ...
doi:10.2174/157016411795678020
pmid:23002391
pmcid:PMC3448448
fatcat:4xvdmkdxufe4xhdswqrt3zpk4u
Computational prediction of proteotypic peptides for quantitative proteomics
2006
Nature Biotechnology
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Several mass spectrometry-based quantitative proteomics methods attempt to comprehensively identify and quantify constituent proteins in complex mixtures 2,3 . ...
Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the ...
ACKNOWLEDGMENTS The authors are grateful to Julien Gagneur for fruitful discussions and the Cellzome biochemistry, mass spectrometry and informatics teams for generating and managing data. ...
doi:10.1038/nbt1275
pmid:17195840
fatcat:aqfp3cpsqfggrmvnbmqua6zwk4
Capture and analysis of quantitative proteomic data
2007
Proteomics
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A variety of tools and approaches are available, in part restricted by the nature of the experiment to be performed and available instrumentation. ...
These tools must deal with a variety of issues, including identification of labelled and unlabelled peptide species, location of the corresponding mass spectrometry scans in the experiment, construction ...
,including ExGen grant EGM17685 to KLW and SJH, BBSB17204 (ISPIDER) to JAS and SJH, Pedro (BBSB12407) to ARJ, SJH, and the BBSRC funded Manchester Centre for Integrative Systems Biology which supports ...
doi:10.1002/pmic.200700127
pmid:17640002
pmcid:PMC2260796
fatcat:dah5ykur4nazthkqivfy73rqeq
MARQUIS: A multiplex method for absolute quantification of peptides and posttranslational modifications
2015
Nature Communications
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To address these issues, we have developed MARQUIS -Multiplex Absolute Regressed Quantification with Internal Standards -a novel mass spectrometry-based approach using a combination of isobaric tags and ...
Absolute quantification of protein expression and post-translational modifications by mass spectrometry has been challenging due to a variety of factors, including the potentially large dynamic range of ...
This work was supported by in part by a grant from the US-Israel Binational Science Foundation and by NIH grants U54 CA112967, R01 CA118705, and R01 CA096504. ...
doi:10.1038/ncomms6924
pmid:25581283
pmcid:PMC4293043
fatcat:6clwhwhkqjfotdolwvzrg6f7hu
Targeted proteomics by selected reaction monitoring mass spectrometry: applications to systems biology and biomarker discovery
2011
Molecular Biosystems
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Mass Spectrometry-based proteomics is now considered a relatively established strategy for protein analysis, ranging from global expression profiling to the identification of protein complexes and specific ...
Recently, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) has become increasingly popular in proteome research for the targeted quantification of proteins and post-translational modifications. ...
In fact, a study by the Aebersold group has shown that neither approach can be generally favoured for absolute protein quantification. 67 In an effort to compare the two quantification platforms, the ...
doi:10.1039/c0mb00159g
pmid:20976349
fatcat:wbuf5ndaargvtndoka3m5x7wsq
Nonparametric Bayesian Evaluation of Differential Protein Quantification
2013
Journal of Proteome Research
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Arbitrary cutoffs are ubiquitous in quantitative computational proteomics: maximum acceptable MS/MS PSM or peptide q value, minimum ion intensity to calculate a fold change, the minimum number of peptides ...
Here we introduce a novel experimental setup and nonparametric Bayesian algorithm for determining the statistical quality of a proposed differential set of proteins or peptides. ...
This work was also supported by a grant from the Swedish Research Council (L.K.). Thanks to Manor Askenazi for his suggestion to use the isotope peaks to generate an empirical null in future work. ...
doi:10.1021/pr400678m
pmid:24024742
pmcid:PMC3824391
fatcat:stjruugz7bhp5hnt24j4rdea3u
On-Beads Digestion in Conjunction with Data-Dependent Mass Spectrometry: A Shortcut to Quantitative and Dynamic Interaction Proteomics
2014
Biology
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In this study, we demonstrate that a quantitative interaction proteomic approach, combining immunoprecipitation, in-solution digestion and label-free quantification mass spectrometry, provides data of ...
approach a suitable method to generate data for system biology approaches. ...
Although mass spectrometry is inherently non-quantitative, several approaches have been developed which allow relative and absolute quantification of peptides and by extension, of the proteins they have ...
doi:10.3390/biology3020320
pmid:24833512
pmcid:PMC4085610
fatcat:wlt536hobne2hoot2kdosds4im
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
2020
International Journal of Molecular Sciences
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We conclude with a discussion of how quantitative protein data can be used to reconstruct protein interactions and signaling networks. ...
We first introduce bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then we review the different statistical and machine learning methods ...
the same level through parametric transformations and maximum likelihood estimation. ...
doi:10.3390/ijms21082873
pmid:32326049
pmcid:PMC7216093
fatcat:5zbrkah4xvec3mq3ypal7cxfbu
Novel approaches for the identification of biomarkers of aggressive prostate cancer
2013
Genome Medicine
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Rapid advances in molecular technologies are likely to lead to signifi cant progress in the foreseeable future. ...
, all of which contribute to the lack of well-defi ned and validated prognostic biomarkers. ...
YK is a recipient of an Ontario Graduate Scholarship. This work was supported by a grant from the Canadian Institute of Health Research (MOP-93772) to TK. ...
doi:10.1186/gm460
pmid:23809668
pmcid:PMC3706951
fatcat:hepyeeftn5hnjo226t7f4jatd4
Combinatorics and next-generation sequencing
2009
Nature Biotechnology
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Quantitative mass spectrometry is now poised to routinely provide such data at large scale and with high accuracy-a testament to the rapid progress in quantitative shotgun proteomics over the last few ...
Nonetheless, given that these approaches offer protein quantification without the need for genetic modification or extensive isotopic labeling, the combination of approaches presented by Malmström et ...
doi:10.1038/nbt0909-826
pmid:19741641
fatcat:iuaenwxfwvcodeat27uf6l2v2m
Quantitative mass spectrometry-based techniques for clinical use: Biomarker identification and quantification☆
2009
Journal of chromatography. B
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MS-based methods for high throughput protein identification and quantification are now available such that the issues arising from the huge dynamic range of proteins present in plasma may be overcome, ...
Recent advances in mass spectrometric (MS) techniques, liquid phase analyte separation and bioinformatic tools for high throughput now mean that this goal may soon become a reality. ...
Variations on the internal standard method have been developed for use in proteomics, including AQUA (absolute quantification of proteins) [87] , PC-IDMS (protein cleavage-isotope dilution mass spectrometry ...
doi:10.1016/j.jchromb.2008.11.023
pmid:19058768
pmcid:PMC7185464
fatcat:2fxm6uvv5bhm3djbg55xuxcbwu
Mass Spectrometric Quantification of N-Linked Glycans by Reference to Exogenous Standards
2016
Journal of Proteome Research
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Mass spectrometry, on the other hand, has generally been limited to relative quantification in which the contribution of the signal intensity for an individual glycan is expressed as a percent of the signal ...
We have investigated whether MS-based glycomics is amenable to absolute quantification by referencing signal intensities to well-characterized oligosaccharide standards. ...
The authors gratefully acknowledge the assistance in acquiring glycan standards provided by Nahid Razi and by the Steering Committee of the Consortium for Functional Glycomics and by James Paulson of The ...
doi:10.1021/acs.jproteome.6b00132
pmid:27432553
pmcid:PMC5501980
fatcat:7jemife47jgpncfhbkyzhn6kle
Targeted proteome investigation via selected reaction monitoring mass spectrometry
2012
Journal of Proteomics
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Due to the enormous complexity of proteomes which constitute the entirety of protein species expressed by a certain cell or tissue, proteome-wide studies performed in discovery mode are still limited in ...
This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry. ...
Acknowledgments We would like to thank the whole Aebersold
R E F E R E N C E S ...
doi:10.1016/j.jprot.2012.04.048
pmid:22579752
fatcat:2sl6xwfhmjhc3ddvmnfynuta4a
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