Targeted proteomics is characterized by a mass spectrometry (MS)-based analysis of defined proteins of interest achieved by quantitation of a pre-selected set of peptides in a complex mixture derived from enzymatic digestion. One major challenge is the selection of suitable peptides that fulfill certain criteria. The most important parameters required are MS-compatibility for maximum sensitivity and robustness as well as uniqueness for target specificity. One of the most sensitive, accurate, and reproducible approaches is selected reaction monitoring (SRM) mass spectrometry. The most suitable MS instrument for the SRM strategy is a triple quadrupole (QqQ-MS). It transmits a peptide precursor ion in Q1 that is then fragmented in q2 and a single peptide fragment ion is selected in Q3 for quantitation. The precursor and fragment ion pair is referred to as a transition and its abundance is used to quantify the abundance of a protein. During an SRM experiment, sequential gating of precursor and product ions in a QqQ-MS allows thousands of precursor/fragment ion combinations (transitions) to be assessed in complex peptide mixtures generated by proteolysis of protein extracts from cells. This combination of filters gives SRM approaches their power in complex samples and allows quantification of many different (including low abundance) proteins over 4 orders of magnitude in crude whole protein extracts from plant tissue samples.
Pioneering work in 2008 first applied SRM mass spectrometry to quantify protein abundance in Arabidopsis and Medicago and since then a large number of other SRM assays have been developed for proteins in a wide variety of species. The impact this approach has had on plant science is undeniable and it was awarded the 2012 Nature Methods “Method of the Year”. However, the ability to quantify all proteins in all species by SRM mass spectrometry in plants has yet to be realized. To achieve this, researchers in the field need to come together to collate their individual peptide or SRM assays and share these with the wider research community.
In recent years targeted proteomics has diversified somewhat to include approaches comparable to SRM. Parallel reaction monitoring (PRM) wherein all precursor transitions are monitored in parallel has been accepted particularly on a QqOrbi MS and has found application in plants. The targeted extraction of precursor transitions from data-independent acquisition (DIA) once-and-forever datasets is another innovative example that holds promise.
This Research Topic provides an opportunity to bring together the current advances in plant targeted mass spectrometry of peptides/proteins with research tools and databases that have been developed to enable the plant science researchers to embrace this highly effective method of protein quantitation.
Targeted proteomics is characterized by a mass spectrometry (MS)-based analysis of defined proteins of interest achieved by quantitation of a pre-selected set of peptides in a complex mixture derived from enzymatic digestion. One major challenge is the selection of suitable peptides that fulfill certain criteria. The most important parameters required are MS-compatibility for maximum sensitivity and robustness as well as uniqueness for target specificity. One of the most sensitive, accurate, and reproducible approaches is selected reaction monitoring (SRM) mass spectrometry. The most suitable MS instrument for the SRM strategy is a triple quadrupole (QqQ-MS). It transmits a peptide precursor ion in Q1 that is then fragmented in q2 and a single peptide fragment ion is selected in Q3 for quantitation. The precursor and fragment ion pair is referred to as a transition and its abundance is used to quantify the abundance of a protein. During an SRM experiment, sequential gating of precursor and product ions in a QqQ-MS allows thousands of precursor/fragment ion combinations (transitions) to be assessed in complex peptide mixtures generated by proteolysis of protein extracts from cells. This combination of filters gives SRM approaches their power in complex samples and allows quantification of many different (including low abundance) proteins over 4 orders of magnitude in crude whole protein extracts from plant tissue samples.
Pioneering work in 2008 first applied SRM mass spectrometry to quantify protein abundance in Arabidopsis and Medicago and since then a large number of other SRM assays have been developed for proteins in a wide variety of species. The impact this approach has had on plant science is undeniable and it was awarded the 2012 Nature Methods “Method of the Year”. However, the ability to quantify all proteins in all species by SRM mass spectrometry in plants has yet to be realized. To achieve this, researchers in the field need to come together to collate their individual peptide or SRM assays and share these with the wider research community.
In recent years targeted proteomics has diversified somewhat to include approaches comparable to SRM. Parallel reaction monitoring (PRM) wherein all precursor transitions are monitored in parallel has been accepted particularly on a QqOrbi MS and has found application in plants. The targeted extraction of precursor transitions from data-independent acquisition (DIA) once-and-forever datasets is another innovative example that holds promise.
This Research Topic provides an opportunity to bring together the current advances in plant targeted mass spectrometry of peptides/proteins with research tools and databases that have been developed to enable the plant science researchers to embrace this highly effective method of protein quantitation.
