Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

Percy, Andrew J.; Tamura-Wells, Jessica; Albar, Juan Pablo; Aloria, Kerman; Amirkhani, Ardeshir; Araújo, Gabriel; Arizmendi, Jesús M.; Blanco, Francisco J.; Canals, Françesc; Cho, Jin Young; Colomé-Calls, Núria; Corrales, Fernando J.; Domont, Gilberto B.; Espadas, Guadalupe; Fernández-Puente, Patricia; Gil, Concha; Haynes, Paul A.; Hernáez, María Luisa; Kim, Jin Young; Kopylov, Arthur T.; Marcilla, Miguel; McKay, Matthew J.; Mirzaei, Mehdi; Molloy, Mark P.; Ohlund, Leanne; Paik, Young Ki; Paradela, Alberto; Raftery, Mark J.; Sabidó, Eduard; Sleno, Lekha; Wilffert, Daniel; Wolters, Justina C.; Yoo, Jong Shin; Zgoda, Victor G.; Parker, Carol E.; Borchers, Christoph H.

doi:10.1016/j.euprot.2015.06.001

Cited by 34 publications

(55 citation statements)

References 21 publications

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“…20 fmol/ μ L to 200 pmol/ μ L (see Table ). All of these proteins are part of the PeptiQuant Workflow Performance Kit (MRM Proteomics, catalogue number WFPK‐A6495‐1) used to monitor LC/MRM–MS performance . For each protein, one proteotypic surrogate peptide was chosen.…”

Section: Methodsmentioning

confidence: 99%

ExSTA: External Standard Addition Method for Accurate High‐Throughput Quantitation in Targeted Proteomics Experiments

Mohammed

Pan

Zhang³

et al. 2017

Proteomics Clinical Apps

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PurposeTargeted proteomics using MRM with stable‐isotope‐labeled internal‐standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard‐addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x‐intercept. Internal NAT‐addition, however, requires multiple analyses of each sample, resulting in increased sample consumption and analysis time.Experimental designTo compare the following three methods, an MRM assay for 34 high‐to‐moderate abundance human plasma proteins is used: classical internal SIS‐addition, internal NAT‐addition, and external NAT‐addition—generated in buffer using NAT and SIS peptides. Using endogenous‐free chicken plasma, the accuracy is also evaluated.ResultsThe internal NAT‐addition outperforms the other two in precision and accuracy. However, the curves derived by internal vs. external NAT‐addition differ by only ≈3.8% in slope, providing comparable accuracies and precision with good CV values.Conclusions and clinical relevanceWhile the internal NAT‐addition method may be “ideal”, this new external NAT‐addition can be used to determine the concentration of high‐to‐moderate abundance endogenous plasma proteins, providing a robust and cost‐effective alternative for clinical analyses or other high‐throughput applications.

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Section: Methodsmentioning

confidence: 99%

ExSTA: External Standard Addition Method for Accurate High‐Throughput Quantitation in Targeted Proteomics Experiments

Mohammed

Pan

Zhang³

et al. 2017

Proteomics Clinical Apps

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show abstract

“…While this variability may satisfy the guidelines for Tier 1 and 2 assays, it is unsuitable for clinical practice. For some methods, large-scale analyses of quantitative proteomic assays have been performed across independent laboratories using a diverse set of LC-MS platforms [64,[112][113][114][115]. These studies have collectively demonstrated the feasibility in measuring a broad range of plasma proteins (encompassing high-to-low abundance) using standardized practices for system suitability, quality control, and quantitative analysis.…”

Section: Expert Commentarymentioning

confidence: 99%

Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential

Percy¹,

Byrns

Pennington

et al. 2016

Expert Review of Proteomics

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This article reviews the status, challenges, requirements, and potential of translating current, MS-based methods to the clinical laboratory. The described methods are discussed and contrasted within a fit-for-purpose approach, while different resources for quality control, quantitative analysis, and data interpretation are additionally provided. Expert commentary: Although great strides have been made over the past five years in developing reliable quantitative assays for plasma protein biomarkers, it is crucial for investigators to have an understanding of the clinical validation process, a major roadblock in translational research. Continued progress in method design and validation of protein assays is necessary to ultimately achieve widespread adoption and regulatory approval.

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“…With the recent advances in SRM technology, front‐end sample preparation, and bioinformatics tools (e.g., Skyline , QuaSAR , and Qualis‐SIS ), SRM‐based targeted proteomics technique is nearly mature for routinely reliable quantification of 10–100 s of target proteins in complex biological samples . In recent years studies for systematic evaluation of SRM assays and their performance have been conducted, such as developing a system suitability protocol for quantitative assessment of intra‐ and inter‐laboratory instrument performance in LC‐SRM analysis , large‐scale development of standardized SRM assays , inter‐laboratory evaluation of SISCAPA‐SRM , and defining three tiers of SRM assays using a “fit‐for‐purpose” approach . In 2012 targeted proteomics was selected as Method of the Year in Nature Methods .…”

Section: Recent Advances In Srm Sensitivity and Its Applicationmentioning

confidence: 99%

Advances in targeted proteomics and applications to biomedical research

et al. 2016

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Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.

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Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

Cited by 34 publications

References 21 publications

ExSTA: External Standard Addition Method for Accurate High‐Throughput Quantitation in Targeted Proteomics Experiments

ExSTA: External Standard Addition Method for Accurate High‐Throughput Quantitation in Targeted Proteomics Experiments

Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential

Advances in targeted proteomics and applications to biomedical research

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