When applied to the relative quantification of a publicly available benchmark dataset, APEX-SMT could provide comparable accuracy to APEX. All these results suggest that APEX-SMT is a promising alternative to APEX for proteome quantification.Analyst...
The significance of individual label-free quantifications was obtained via a t test approach. For a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. MaxLFQ is a generic label-free quantification ...
Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset J. Proteomics, 132 (2016), pp. 51-62 View PDFView articleView in ScopusGoogle Scholar 27 T. Välikangas, T. Suomi, L.L. Elo A systematic evaluation of normalization methods...
Quantitative proteomics is key for basic research, but needs improvements to satisfy an increasing demand for large sample series in diagnostics, academia and industry. A switch from nanoflowrate to microflowrate chromatography can improve throughput and reduce costs. However, concerns about undersamplin...
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics Main Genomics and proteomics offer immense potential for enhancing human health and the environment. For example, next-generation sequencing has revolutionized genomics by making DNA and RNA sequencing much faster and...
Thus, for the virus dataset, 207 actual proteins correspond to 252 locative proteins; and for the plant dataset, 978 actual proteins correspond to 1055 locative proteins. The breakdown of these two benchmark datasets were shown in Table2(a) and Table2(b). In statistical prediction, leave-one...
Imputation techniques provide means to replace missing measurements with a value and are used in almost all downstream analysis of mass spectrometry (MS) based proteomics data using label-free quantification (LFQ). Here we demonstrate how collaborative f
The significance of individual label-free quantifications was obtained via a t test approach. For a second benchmark dataset, we accurately quantify fold changes over several orders of magnitude, a task that is challenging with label-based methods. MaxLFQ is a generic label-free ...
Here we carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n = 67, including individuals with health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics ...
Sensitive and spatial exploration of the metabolism of tumors at the metabolome level is highly challenging. In this study, we developed an in situ metabolomics method based on ambient mass spectrometry imaging using air flow-assisted desorption electros