King's College London

Research portal

Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments

Research output: Contribution to journalLiterature review

Standard

Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments. / Thompson, Andrew J.; Abu, Mika; Hanger, Diane P.

In: AMINO ACIDS, Vol. 43, No. 3, 09.2012, p. 1075-1085.

Research output: Contribution to journalLiterature review

Harvard

Thompson, AJ, Abu, M & Hanger, DP 2012, 'Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments', AMINO ACIDS, vol. 43, no. 3, pp. 1075-1085. https://doi.org/10.1007/s00726-012-1287-x

APA

Thompson, A. J., Abu, M., & Hanger, D. P. (2012). Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments. AMINO ACIDS, 43(3), 1075-1085. https://doi.org/10.1007/s00726-012-1287-x

Vancouver

Thompson AJ, Abu M, Hanger DP. Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments. AMINO ACIDS. 2012 Sep;43(3):1075-1085. https://doi.org/10.1007/s00726-012-1287-x

Author

Thompson, Andrew J. ; Abu, Mika ; Hanger, Diane P. / Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments. In: AMINO ACIDS. 2012 ; Vol. 43, No. 3. pp. 1075-1085.

Bibtex Download

@article{33b859b5c0094decafae1612788bb56e,
title = "Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments",
abstract = "Proteomic technologies have matured to a level enabling accurate and reproducible quantitation of peptides and proteins from complex biological matrices. Analysis of samples as diverse as assembled protein complexes, whole cell lysates or sub-cellular proteomes from cell cultures, and direct analysis of animal and human tissues and fluids demonstrate the incredible versatility of the fundamental nature of the technique that forms the basis of most proteomic applications today (mass spectrometry). Determining the mass of biomolecules and their fragments or related products with high accuracy can convey a highly specific assay for detection and identification. Importantly, ion currents representative of these specifically identified analytes can be accurately quantified with the correct application of smart isobaric tagging chemistries, heavy and light isotopically derivatised samples or standards, or by careful application of workflows to compare unlabelled samples in so-called 'label-free' and targeted selected reaction monitoring experiments. In terms of exploring biology, a myriad of protein changes and modifications are being increasingly probed and quantified, including diverse chemical changes from relatively decisive modifications such as protein splicing and truncation, to more transient dynamic modifications such as phosphorylation, acetylation and ubiquitination. Proteomic workflows can be complex beasts and several key considerations to ensure effective applications have been outlined in the recent literature. The past year has witnessed the publication of several excellent reviews that thoroughly describe the fundamental principles underlying the state of the art. This review further elaborates on specific critical issues introduced by these publications and raises other important unaddressed considerations and new developments that directly impact on the effectiveness of proteomic technologies, in particular for, but not necessarily exclusive to peptide-centric experiments. These factors are discussed both in terms of qualitative analyses, including dynamic range and sampling issues, and developments to improve the translation of peptide fragmentation data into peptide and protein identities, as well as quantitative analyses, including data normalisation and the utility of ontology or functional annotation, the effects of modified peptides, and considered experimental design to facilitate the use of robust statistical methods.",
author = "Thompson, {Andrew J.} and Mika Abu and Hanger, {Diane P.}",
year = "2012",
month = sep,
doi = "10.1007/s00726-012-1287-x",
language = "English",
volume = "43",
pages = "1075--1085",
journal = "AMINO ACIDS",
issn = "0939-4451",
publisher = "Springer Wien",
number = "3",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Key issues in the acquisition and analysis of qualitative and quantitative mass spectrometry data for peptide-centric proteomic experiments

AU - Thompson, Andrew J.

AU - Abu, Mika

AU - Hanger, Diane P.

PY - 2012/9

Y1 - 2012/9

N2 - Proteomic technologies have matured to a level enabling accurate and reproducible quantitation of peptides and proteins from complex biological matrices. Analysis of samples as diverse as assembled protein complexes, whole cell lysates or sub-cellular proteomes from cell cultures, and direct analysis of animal and human tissues and fluids demonstrate the incredible versatility of the fundamental nature of the technique that forms the basis of most proteomic applications today (mass spectrometry). Determining the mass of biomolecules and their fragments or related products with high accuracy can convey a highly specific assay for detection and identification. Importantly, ion currents representative of these specifically identified analytes can be accurately quantified with the correct application of smart isobaric tagging chemistries, heavy and light isotopically derivatised samples or standards, or by careful application of workflows to compare unlabelled samples in so-called 'label-free' and targeted selected reaction monitoring experiments. In terms of exploring biology, a myriad of protein changes and modifications are being increasingly probed and quantified, including diverse chemical changes from relatively decisive modifications such as protein splicing and truncation, to more transient dynamic modifications such as phosphorylation, acetylation and ubiquitination. Proteomic workflows can be complex beasts and several key considerations to ensure effective applications have been outlined in the recent literature. The past year has witnessed the publication of several excellent reviews that thoroughly describe the fundamental principles underlying the state of the art. This review further elaborates on specific critical issues introduced by these publications and raises other important unaddressed considerations and new developments that directly impact on the effectiveness of proteomic technologies, in particular for, but not necessarily exclusive to peptide-centric experiments. These factors are discussed both in terms of qualitative analyses, including dynamic range and sampling issues, and developments to improve the translation of peptide fragmentation data into peptide and protein identities, as well as quantitative analyses, including data normalisation and the utility of ontology or functional annotation, the effects of modified peptides, and considered experimental design to facilitate the use of robust statistical methods.

AB - Proteomic technologies have matured to a level enabling accurate and reproducible quantitation of peptides and proteins from complex biological matrices. Analysis of samples as diverse as assembled protein complexes, whole cell lysates or sub-cellular proteomes from cell cultures, and direct analysis of animal and human tissues and fluids demonstrate the incredible versatility of the fundamental nature of the technique that forms the basis of most proteomic applications today (mass spectrometry). Determining the mass of biomolecules and their fragments or related products with high accuracy can convey a highly specific assay for detection and identification. Importantly, ion currents representative of these specifically identified analytes can be accurately quantified with the correct application of smart isobaric tagging chemistries, heavy and light isotopically derivatised samples or standards, or by careful application of workflows to compare unlabelled samples in so-called 'label-free' and targeted selected reaction monitoring experiments. In terms of exploring biology, a myriad of protein changes and modifications are being increasingly probed and quantified, including diverse chemical changes from relatively decisive modifications such as protein splicing and truncation, to more transient dynamic modifications such as phosphorylation, acetylation and ubiquitination. Proteomic workflows can be complex beasts and several key considerations to ensure effective applications have been outlined in the recent literature. The past year has witnessed the publication of several excellent reviews that thoroughly describe the fundamental principles underlying the state of the art. This review further elaborates on specific critical issues introduced by these publications and raises other important unaddressed considerations and new developments that directly impact on the effectiveness of proteomic technologies, in particular for, but not necessarily exclusive to peptide-centric experiments. These factors are discussed both in terms of qualitative analyses, including dynamic range and sampling issues, and developments to improve the translation of peptide fragmentation data into peptide and protein identities, as well as quantitative analyses, including data normalisation and the utility of ontology or functional annotation, the effects of modified peptides, and considered experimental design to facilitate the use of robust statistical methods.

U2 - 10.1007/s00726-012-1287-x

DO - 10.1007/s00726-012-1287-x

M3 - Literature review

VL - 43

SP - 1075

EP - 1085

JO - AMINO ACIDS

JF - AMINO ACIDS

SN - 0939-4451

IS - 3

ER -

View graph of relations

© 2020 King's College London | Strand | London WC2R 2LS | England | United Kingdom | Tel +44 (0)20 7836 5454