SRM-MS Applications in Proteomics
Selected reaction monitoring mass spectrometry (SRM-MS) with its recent advantages has opened new avenues for widespread use of biological applications in proteomics. In general proteomics area, applications include protein abundance studies, protein modi
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SRM-MS Applications in Proteomics
Selected reaction monitoring mass spectrometry (SRM-MS) has been developed for proteomics over the last 20 years with advanced instrumentation, diverse sample preparation techniques, and user-friendly bioinformatics tools. The SRM technique itself also evaluated systematically for assay robustness, reproducibility, and interchangeability among laboratories (Addona et al. 2009; Prakash et al. 2012). It has several competitive advantages in terms of its multiplexing capability, assay specificity, overall method development time for the new protein targets when compared to contemporary techniques including ELISA (Shi et al. 2016). In recent years, mostly facilitated by the improvements in instrumentation and software, applications of SRM-MS have been increased rapidly in the diverse areas of biology and biomedical fields for specific, reproducible, and quantitative measurement in changes of peptides and modified peptides on interest (Carr et al. 2014). Successful application of targeted proteomics including SRM-MS depends on the ability to generate reliable assays that accurately and confidently identify target peptides in a sample; however, until recently, there was no mass speccommunity-wide consensus on the acceptable criteria of a reliable assay and impact of variable criteria on the quality of the ultimate assay results (Carr et al. 2014). Besides, most of the time, research papers on targeted proteomics do not contain adequate assay information for readers or reviewers to be confident enough on the methodology/results, or for other researchers to exactly reproduce the assays. A few years ago, the mass spec community addressed this issue and took initiative to develop a clear and consensus guideline that includes “fit-forpurpose” approach defining three tiers of assays differentiated by their performance and the extent of analytical characterization, and the minimum assay information requirements for the publication in peer-reviewed journals (Carr et al. 2014). At the top levels, Tiers 1 and 2 consist of two distinct properties that differ from discovery-type experiments—ability to repeatedly measure sets of analytes of interest within and across assays and utilize internal standards for every analyte for confident detection and precise quantification. Tier 3 assays enable repeated
© Springer Nature Switzerland AG 2020 M. Hossain, Selected Reaction Monitoring Mass Spectrometry (SRM-MS) in Proteomics, https://doi.org/10.1007/978-3-030-53433-2_7
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7 SRM-MS Applications in Proteomics
measurement of the same sets of experiments but without any internal standard that can be utilized in the initial stage of biological studies (Carr et al. 2014).
7.1 General Proteomic Applications Since its development for proteomics, SRM-MS has been applied to a variety of questions in biological fields, including protein abundance studies, protein modification studies, system biology or protein network biology, etc. Protein abundance studies have been reviewed extensively in Ebhardt
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