Automation, parallelism, and robotics for proteomics

Abstract

The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomicsbased information with other related research areas.

One-by-One Sample Preparation Method for Protein Network Analysis

“…To realize the one-by-one concept and perform a pilot feasibility study, a fully automated sample preparation system is required. However, in the proteomics field, partial automation for parallel preparation is usually only applied to save analysis time, to eliminate sample contamination, and to reduce human error (Alterovitz et al, 2006). Several semi-automated robots that are specialized in certain processes are commercially available, such as liquid dispenser robots, cell culture robots, and electrophoresis gel cutting robots.…”

Automated Calculation of Unique PeptideSequencesforUnambiguous Identification of HighlyHomologousProteins byMassSpectrometry

“…However, performing BLAST searches manually in order to identify unique peptides is both tedious and time-consuming. Nowadays sample preparation, nanoHPLC, mass spectrometry and protein identification in modern proteomics can be automated (Alterovitz et al, 2006) , but to our knowledge no software is available for automated exact calculation of unique peptides for unambiguous identification of proteins. Here we report the construction of a software tool, which is called Unique Peptide Finder (UPF).…”

Monolith‐based immobilized enzyme reactors: Recent developments and applications for proteome analysis

“…Therefore, multidisciplinary efforts are indispensable for proteome analysis. To accelerate the proteomics study, high-efficient separation, high-sensitive characterization, and high-throughput analysis are urgently required [78]. Although 2-DE has firmly held an important position in proteomic analysis because of its unparalleled resolving power, it is manual, time-consuming, has poor sensitivity, poor quantification, and limited dynamic range.…”