Standard Flow Multiplexed Proteomics (SFloMPro)—An Accessible Alternative to NanoFlow Based Shotgun Proteomics

Multiplexed proteomics using isobaric tagging allows for simultaneously comparing the proteomes of multiple samples. In this technique, digested peptides from each sample are labeled with a chemical tag prior to pooling sample for LC-MS/MS with nanoflow chromatography (NanoLC). The isobaric nature of the tag prevents deconvolution of samples until fragmentation liberates the isotopically labeled reporter ions. To ensure efficient peptide labeling, large concentrations of labeling reagents are included in the reagent kits to allow scientists to use high ratios of chemical label per peptide. The increasing speed and sensitivity of mass spectrometers has reduced the peptide concentration required for analysis, leading to most of the label or labeled sample to be discarded. In conjunction, improvements in the speed of sample loading, reliable pump pressure, and stable gradient construction of analytical flow HPLCs has continued to improve the sample delivery process to the mass spectrometer. In this study we describe a method for performing multiplexed proteomics without the use of NanoLC by using offline fractionation of labeled peptides followed by rapid “standard flow” HPLC gradient LC-MS/MS. Standard Flow Multiplexed Proteomics (SFloMPro) enables high coverage quantitative proteomics of up to 16 mammalian samples in about 24 h. In this study, we compare NanoLC and SFloMPro analysis of fractionated samples. Our results demonstrate that comparable data is obtained by injecting 20 µg of labeled peptides per fraction with SFloMPro, compared to 1 µg per fraction with NanoLC. We conclude that, for experiments where protein concentration is not strictly limited, SFloMPro is a competitive approach to traditional NanoLC workflows with improved up-time, reliability and at a lower relative cost per sample.

Standard Flow Multiplexed Proteomics (SFloMPro). An Accessible and Cost-Effective Alternative to NanoLC Workflows

Multiplexed proteomics using isobaric tagging allows for simultaneously comparing the proteomes of multiple samples. In this technique, digested peptides from each sample are labeled with a chemical tag prior to pooling sample for LC-MS/MS with nanoflow chromatography (NanoLC). The isobaric nature of the tag prevents deconvolution of samples until fragmentation liberates the isotopically labeled reporter ions. To ensure efficient peptide labeling, large concentrations of labeling reagents are included in the reagent kits to allow scientists to use high ratios of chemical label per peptide. The increasing speed and sensitivity of mass spectrometers has reduced the peptide concentration required for analysis, leading to most of the label or labeled sample to be discarded. In conjunction, improvements in the speed of sample loading, reliable pump pressure, and stable gradient construction of analytical flow HPLCs has continued to improve the sample delivery process to the mass spectrometer. In this study we describe a method for performing multiplexed proteomics without the use of NanoLC by using offline fractionation of labeled peptides followed by rapid standard flow HPLC gradient LC-MS/MS. Standard Flow Multiplexed Proteomics (SFloMPro) enables high coverage quantitative proteomics of up to 16 mammalian samples in about 24 hours. In this study, we compare NanoLC and SFloMPro analysis of fractionated samples. Our results demonstrate that comparable data is obtained by injecting 20 micrograms of labeled peptides per fraction with SFloMPro, compared to 1 microgram per fraction with NanoLC. We conclude that, for experiments where protein concentration is not strictly limited, SFloMPro is a competitive approach to traditional NanoLC workflows with improved up-time, reliability and at a lower relative cost per sample.

Hormesis and risk communication: a comment to Ortwin Renn

Professor Ortwin Renn should be congratulated for authoring the definitive piece on risk communication with regard to hormesis.1 Most of his conclusions I agree with, specifically the importance of labelling hormesis as a possible natural effect, thereby reducing the stigmatization associated with a technical/chemical label. Rather than discussing all the points that Renn raises, in this comment I will focus on the issue of trust, a topic that Renn does examine but which I feel does not get adequate attention and which I do not completely agree with. In so doing, in my conclusions I am more optimistic than Renn is in preparing risk communication strategies regarding hormesis and other new paradigms to target audiences (defined in most instances as the general public and stakeholders).

Studies directed toward labeling analysis of angiotensin II in plasma.

We assay a 1-mL plasma sample containing angiotensin II (103 pg by radioimmunoassay) for the hormone by the following sequence of steps: add 125I-labeled val5-angiotensin II as an internal standard, extract on a C18 Sep Pak column, extract on an antibody affinity column, label the extract with an 125I Bolton-Hunter reagent, separate on a Bio Gel P2 column, and repetitively separate on a reversed-phase "high-performance" liquid-chromatographic column, detecting the eluting compounds by counting radioactivity. The fact that we measured 46 pg of angiotensin II-like substance per milliliter in a sample of pooled plasma is encouraging for the further development of this methodology. In particular, replacing the radioisotope with a more suitable chemical label such as an electrophoric (electron-capturing) release tag should be useful.