Application & Technical Notes

The Gelfree^™ 8100 Fractionation System provides molecular weight-based partitioning of complex biological samples with liquid phase recovery. The high loading capacity permits more starting material, while the resolving power of the system reduces the complexity of the sample for downstream analysis. Whether it’s a bottom-up or top-down workflow, use of the Gelfree system will increase the number and quality of protein identifications and enable better protein characterization. As with all sample preparation tools, the quality of reagents and procedures used before and after Gelfree fractionation dictate the quality of the results.

Fractionation of brain lysate

The Gelfree^™ 8100 Fractionation System provides molecular weight-based partitioning of complex biological samples with liquid phase recovery. The high loading capacity of the system allows one to work with more starting material, while the resolving power of the system reduces the complexity of the sample for downstream analysis. Whether it’s a bottom-up or top-down workflow, use of the Gelfree system will increase the number and quality of protein identifications and enable better protein characterization. As with all sample preparation tools, the quality of reagents and procedures used before and after Gelfree fractionation dictate the quality of the results.

Fractionation of liver lysate

The Gelfree^™ 8100 Fractionation System provides molecular weight-based partitioning of complex biological samples with liquid phase recovery. The high loading capacity of the system allows one to work with more starting material, while the resolving power of the system reduces the complexity of the sample for downstream analysis. Whether it’s a bottom-up or top-down workflow, use of the Gelfree system will increase the number and quality of protein identifications and enable better protein characterization. As with all sample preparation methods, the quality of reagents and procedures used before and after Gelfree fractionation dictate the quality of the results.

Fractionation of S. Cerevisiae

PPS Silent^® Surfactant was designed, synthesized, and characterized as part of a research project to develop MALDI-friendly surfactants to replace common laboratory detergents such as sodium dodecyl sulfate and n-octyl-ß-d-glucopyranoside.1 A principal objective of the project was to enable elimination of detergent properties that interfere with MALDI afterprotein extraction.

Hydrolysis of PPS

PPS Silent® Surfactant, Acid Cleavable Detergent use and storage instructions.

Package Insert : Use and Storage

As a developer of peptide hormone-based medications, Amylin Pharmaceuticals, Inc., has an ongoing strategic interest in optimizing sample preparation of peptide amyloid protein analogues from biological matrices, such as human plasma. Preparing an amyloid peptide extract of suffi cient concentration and purity for LC-MS/MS analysis presents a number of challenges, including poor solubility relating to amyloid hydrophobicity, non specific surface interactions, and the enzymatic activity of human plasma.

Hydrophobic Peptide Extraction

Despite the analytical advantages demonstrated by the use of laser micro-dissection for cell-type specifi c genomic analysis, similarly productive applications of corollary proteomic analysis of microdissected cell populations have been limited. Obtaining high quality proteomic analysis results using nanoLC-MS/MS, a key analytical method of proteomics, has typically required more cells than can readily be collected by laser capture/catapult microdissection (LCM). Additionally, when time or tissue sample sizes are limiting, as is often the case with fresh or frozen clinical specimens, research strategies that rely on pooling cells captured from multiple sections
are unfeasible.

NanoLC-MS/MS Analysis of LCM Samples

Shotgun proteomics has recently emerged as an alternative to gel-based methods for whole-proteome differential expression analysis. A key experimental objective in shotgun proteomics is to identify as many individual proteins as possible in each sample. Increasing the number of identified proteins enables analysis of a higher percentage of the expressed proteome and increases the odds of finding meaningful proteome differences, regulated proteins, and affected pathways.

Shotgun Proteomics

Recent advances in proteomics methods permit quantification of protein expression profiles between different experimental conditions. One such method is isobaric tagging followed by MS/MS analysis for relative and absolute peptide quantification. This quantification technology can be applied to the study of proteomics phenomena such as differential patterns of protein abundance associated with disease states, and up- and down-regulation of protein expression associated with experimentally altered phenotypes.

iTRAQ Analysis of Triton-insoluble membr