A quality control of proteomic experiments based on multiple isotopologous internal standards

Bourmaud, Adèle; Gallien, Sébastien; Domon, Bruno

doi:10.1016/j.euprot.2015.07.010

Cited by 11 publications

(11 citation statements)

References 14 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… 19 , 64 Addition of SIL peptides with different labels at different time points before and after the digestion period enables the comparison of endogenous peptides produced relative to the labeled peptides present during the digestion and thus may be used to demonstrate changes of the (SIL) peptides during the sample preparation workflow. 61 , 65 , 66 Other solutions for internal standard strategies that have been explored are winged peptides (with sequences that still require tryptic cleavage). 67 , 68 Also SIL peptides can be obtained from so-called Protein Epitope Signature Tags (PrESTs), 69 containing a short and unique sequence of a protein of interest which can be produced in E. coli .…”

Section: Achieving Long-term Robustness: Methods Development and Analymentioning

confidence: 99%

The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs

Smit

Ruhaak

Romijn

et al. 2021

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

Protein mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics. In contrast to immunoassays with indirect readouts, MS quantifications are multiplexed and include identification of proteoforms in a direct manner. Although widely used for routine measurements of drugs and metabolites, the number of clinical MS-based protein applications is limited. In this paper, we share our experience and aim to take away the concerns that have kept laboratory medicine from implementing quantitative protein MS. To ensure added value of new medical tests and guarantee accurate test results, five key elements of test evaluation have been established by a working group within the European Federation for Clinical Chemistry and Laboratory Medicine. Moreover, it is emphasized to identify clinical gaps in the contemporary clinical pathways before test development is started. We demonstrate that quantitative protein MS tests that provide an additional layer of clinical information have robust performance and meet long-term desirable analytical performance specifications as exemplified by our own experience. Yet, the adoption of quantitative protein MS tests into medical laboratories is seriously hampered due to its complexity, lack of robotization and high initial investment costs. Successful and widespread implementation in medical laboratories requires uptake and automation of this next generation protein technology by the In-Vitro Diagnostics industry. Also, training curricula of lab workers and lab specialists should include education on enabling technologies for transitioning to precision medicine by quantitative protein MS tests.

show abstract

Section: Achieving Long-term Robustness: Methods Development and Analymentioning

confidence: 99%

The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs

Smit

Ruhaak

Romijn

et al. 2021

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…Application of different techniques for the preparation, decomplexation, and measurement of the venom samples leads to the fact that the data obtained by different research teams may significantly differ. If we then add several various procedures for further data processing, based on distinct concepts and algorithms, it is extremely difficult to draw accurate and reliable conclusions from comparing proteomic data between different studies [9].…”

Section: Introductionmentioning

confidence: 99%

Different Research Approaches in Unraveling the Venom Proteome of Naja ashei

et al. 2020

View full text Add to dashboard Cite

The dynamic development of venomics in recent years has resulted in a significant increase in publicly available proteomic data. The information contained therein is often used for comparisons between different datasets and to draw biological conclusions therefrom. In this article, we aimed to show the possible differences that can arise, in the final results of the proteomic experiment, while using different research workflows. We applied two software solutions (PeptideShaker and MaxQuant) to process data from shotgun LC-MS/MS analysis of Naja ashei venom and collate it with the previous report concerning this species. We were able to provide new information regarding the protein composition of this venom but also present the qualitative and quantitative limitations of currently used proteomic methods. Moreover, we reported a rapid and straightforward technique for the separation of the fraction of proteins from the three-finger toxin family. Our results underline the necessary caution in the interpretation of data based on a comparative analysis of data derived from different studies.

show abstract

“…The spiked DnaK did not affect the digestibility of the sample proteins, nor did the biological matrix affect digestion of DnaK. Therefore, it appears to be a suitable internal digestion control for complex protein mixtures, such as milk and plasma, which should be combined with a mixture of isotopologuos peptides after digestion [23].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Sample Preparation Strategies for Human Milk and Plasma Proteomics

2021

View full text Add to dashboard Cite

Sample preparation is the most critical step in proteomics as it directly affects the subset of proteins and peptides that can be reliably identified and quantified. Although a variety of efficient and reproducible sample preparation strategies have been developed, their applicability and efficacy depends much on the biological sample. Here, three approaches were evaluated for the human milk and plasma proteomes. Protein extracts were digested either in an ultrafiltration unit (filter-aided sample preparation, FASP) or in-solution (ISD). ISD samples were desalted by solid-phase extraction prior to nRPC-ESI-MS/MS. Additionally, milk and plasma samples were directly digested by FASP without prior protein precipitation. Each strategy provided inherent advantages and disadvantages for milk and plasma. FASP appeared to be the most time efficient procedure with a low miscleavage rate when used for a biological sample aliquot, but quantitation was less reproducible. A prior protein precipitation step improved the quantitation by FASP due to significantly higher peak areas for plasma and a much better reproducibility for milk. Moreover, the miscleavage rate for milk, the identification rate for plasma, and the carbamidomethylation efficiency were improved. In contrast, ISD of both milk and plasma resulted in higher miscleavage rates and is therefore less suitable for targeted proteomics.

show abstract

A quality control of proteomic experiments based on multiple isotopologous internal standards

Cited by 11 publications

References 14 publications

The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs

The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs

Different Research Approaches in Unraveling the Venom Proteome of Naja ashei

Evaluation of Sample Preparation Strategies for Human Milk and Plasma Proteomics

Contact Info

Product

Resources

About