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A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry

BACKGROUND: Label-free quantitation of mass spectrometric data is one of the simplest and least expensive methods for differential expression profiling of proteins and metabolites. The need for high accuracy and performance computational label-free quantitation methods is still high in the biomarker...

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Autores principales: Aoshima, Ken, Takahashi, Kentaro, Ikawa, Masayuki, Kimura, Takayuki, Fukuda, Mitsuru, Tanaka, Satoshi, Parry, Howell E, Fujita, Yuichiro, Yoshizawa, Akiyasu C, Utsunomiya, Shin-ichi, Kajihara, Shigeki, Tanaka, Koichi, Oda, Yoshiya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252003/
https://www.ncbi.nlm.nih.gov/pubmed/25420746
http://dx.doi.org/10.1186/s12859-014-0376-0
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author Aoshima, Ken
Takahashi, Kentaro
Ikawa, Masayuki
Kimura, Takayuki
Fukuda, Mitsuru
Tanaka, Satoshi
Parry, Howell E
Fujita, Yuichiro
Yoshizawa, Akiyasu C
Utsunomiya, Shin-ichi
Kajihara, Shigeki
Tanaka, Koichi
Oda, Yoshiya
author_facet Aoshima, Ken
Takahashi, Kentaro
Ikawa, Masayuki
Kimura, Takayuki
Fukuda, Mitsuru
Tanaka, Satoshi
Parry, Howell E
Fujita, Yuichiro
Yoshizawa, Akiyasu C
Utsunomiya, Shin-ichi
Kajihara, Shigeki
Tanaka, Koichi
Oda, Yoshiya
author_sort Aoshima, Ken
collection PubMed
description BACKGROUND: Label-free quantitation of mass spectrometric data is one of the simplest and least expensive methods for differential expression profiling of proteins and metabolites. The need for high accuracy and performance computational label-free quantitation methods is still high in the biomarker and drug discovery research field. However, recent most advanced types of LC-MS generate huge amounts of analytical data with high scan speed, high accuracy and resolution, which is often impossible to interpret manually. Moreover, there are still issues to be improved for recent label-free methods, such as how to reduce false positive/negatives of the candidate peaks, how to expand scalability and how to enhance and automate data processing. AB3D (A simple label-free quantitation algorithm for Biomarker Discovery in Diagnostics and Drug discovery using LC-MS) has addressed these issues and has the capability to perform label-free quantitation using MS1 for proteomics study. RESULTS: We developed an algorithm called AB3D, a label free peak detection and quantitative algorithm using MS1 spectral data. To test our algorithm, practical applications of AB3D for LC-MS data sets were evaluated using 3 datasets. Comparisons were then carried out between widely used software tools such as MZmine 2, MSight, SuperHirn, OpenMS and our algorithm AB3D, using the same LC-MS datasets. All quantitative results were confirmed manually, and we found that AB3D could properly identify and quantify known peptides with fewer false positives and false negatives compared to four other existing software tools using either the standard peptide mixture or the real complex biological samples of Bartonella quintana (strain JK31). Moreover, AB3D showed the best reliability by comparing the variability between two technical replicates using a complex peptide mixture of HeLa and BSA samples. For performance, the AB3D algorithm is about 1.2 - 15 times faster than the four other existing software tools. CONCLUSIONS: AB3D is a simple and fast algorithm for label-free quantitation using MS1 mass spectrometry data for large scale LC-MS data analysis with higher true positive and reasonable false positive rates. Furthermore, AB3D demonstrated the best reproducibility and is about 1.2- 15 times faster than those of existing 4 software tools. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0376-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-42520032014-12-04 A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry Aoshima, Ken Takahashi, Kentaro Ikawa, Masayuki Kimura, Takayuki Fukuda, Mitsuru Tanaka, Satoshi Parry, Howell E Fujita, Yuichiro Yoshizawa, Akiyasu C Utsunomiya, Shin-ichi Kajihara, Shigeki Tanaka, Koichi Oda, Yoshiya BMC Bioinformatics Methodology Article BACKGROUND: Label-free quantitation of mass spectrometric data is one of the simplest and least expensive methods for differential expression profiling of proteins and metabolites. The need for high accuracy and performance computational label-free quantitation methods is still high in the biomarker and drug discovery research field. However, recent most advanced types of LC-MS generate huge amounts of analytical data with high scan speed, high accuracy and resolution, which is often impossible to interpret manually. Moreover, there are still issues to be improved for recent label-free methods, such as how to reduce false positive/negatives of the candidate peaks, how to expand scalability and how to enhance and automate data processing. AB3D (A simple label-free quantitation algorithm for Biomarker Discovery in Diagnostics and Drug discovery using LC-MS) has addressed these issues and has the capability to perform label-free quantitation using MS1 for proteomics study. RESULTS: We developed an algorithm called AB3D, a label free peak detection and quantitative algorithm using MS1 spectral data. To test our algorithm, practical applications of AB3D for LC-MS data sets were evaluated using 3 datasets. Comparisons were then carried out between widely used software tools such as MZmine 2, MSight, SuperHirn, OpenMS and our algorithm AB3D, using the same LC-MS datasets. All quantitative results were confirmed manually, and we found that AB3D could properly identify and quantify known peptides with fewer false positives and false negatives compared to four other existing software tools using either the standard peptide mixture or the real complex biological samples of Bartonella quintana (strain JK31). Moreover, AB3D showed the best reliability by comparing the variability between two technical replicates using a complex peptide mixture of HeLa and BSA samples. For performance, the AB3D algorithm is about 1.2 - 15 times faster than the four other existing software tools. CONCLUSIONS: AB3D is a simple and fast algorithm for label-free quantitation using MS1 mass spectrometry data for large scale LC-MS data analysis with higher true positive and reasonable false positive rates. Furthermore, AB3D demonstrated the best reproducibility and is about 1.2- 15 times faster than those of existing 4 software tools. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0376-0) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-25 /pmc/articles/PMC4252003/ /pubmed/25420746 http://dx.doi.org/10.1186/s12859-014-0376-0 Text en © Aoshima et al.; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Aoshima, Ken
Takahashi, Kentaro
Ikawa, Masayuki
Kimura, Takayuki
Fukuda, Mitsuru
Tanaka, Satoshi
Parry, Howell E
Fujita, Yuichiro
Yoshizawa, Akiyasu C
Utsunomiya, Shin-ichi
Kajihara, Shigeki
Tanaka, Koichi
Oda, Yoshiya
A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
title A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
title_full A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
title_fullStr A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
title_full_unstemmed A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
title_short A simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
title_sort simple peak detection and label-free quantitation algorithm for chromatography-mass spectrometry
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4252003/
https://www.ncbi.nlm.nih.gov/pubmed/25420746
http://dx.doi.org/10.1186/s12859-014-0376-0
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