Abstract
Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
| Original language | English |
|---|---|
| Pages (from-to) | 161-197 |
| Number of pages | 37 |
| Journal | Methods In Molecular Biology (Clifton, N.J.) |
| Volume | 2051 |
| DOIs | |
| Publication status | Published - 1 Jan 2020 |
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Keywords
- Label-free quantitation
- Liquid chromatography
- Mass spectrometry
- Peptide quantitation
- Protein quantitation
- Stable isotope labeling
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Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. / Matthiesen, Rune; Carvalho, Ana Sofia.
In: Methods In Molecular Biology (Clifton, N.J.), Vol. 2051, 01.01.2020, p. 161-197.Research output: Contribution to journal › Article
TY - JOUR
T1 - Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry
AU - Matthiesen, Rune
AU - Carvalho, Ana Sofia
PY - 2020/1/1
Y1 - 2020/1/1
N2 - Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
AB - Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
KW - Label-free quantitation
KW - Liquid chromatography
KW - Mass spectrometry
KW - Peptide quantitation
KW - Protein quantitation
KW - Stable isotope labeling
UR - http://www.scopus.com/inward/record.url?scp=85072605998&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-9744-2_7
DO - 10.1007/978-1-4939-9744-2_7
M3 - Article
VL - 2051
SP - 161
EP - 197
JO - Methods In Molecular Biology (Clifton, N.J.)
JF - Methods In Molecular Biology (Clifton, N.J.)
SN - 1064-3745
ER -