PROTEOMICS

Cover image for Vol. 14 Issue 23-24

Edited By: Michael J. Dunn

Impact Factor: 3.973

ISI Journal Citation Reports © Ranking: 2013: 14/78 (BIOCHEMICAL RESEARCH METHODS); 87/291 (Biochemistry & Molecular Biology)

Online ISSN: 1615-9861

Associated Title(s): PROTEOMICS - Clinical Applications

8_18/2008Cover Picture: Proteomics 18/2008

In this issue of Proteomics you will find the following highlighted articles:

Flying through fixing formalin

There's no free lunch – whether social or scientific. If you want the long term stability of formalin, you give up the flexibility of fresh frozen tissue. Or do you? Groseclose et al. report here on preparing tissue arrays from formalin-fixed, paraffin embedded material for MALDI MS imaging. The key is the number of procedures that can now be performed on the embedded section. In situ digestion with proteases, including trypsin, and direct deposition of matrix on the tissue array section gave good quality data that could be used for database searching and for MS/MS sequencing. Mass spectrometer imaging data could distinguish subsets of markers that distinguish tissue of origin and indicate type and stage of carcinomas. For a reliable set of marker proteins, a much larger set of samples (>10×) must be tested.

Groseclose, M. R. et al., Proteomics 2008, 8, 3715–3724.

MALDI-TOF MS Imaging: worth waiting for

We've all seen movies where the clues to who committed the nasty deed seem to take forever to appear. Initial peptide imaging by MS seemed to be that way. The objective of this study by Minerva et al. was to optimize the protocol for MS imaging (MSI) of thin section samples by MALDI-TOF. Using pancreas tissue samples, which have cells with a variety of well studied peptides (e.g. pancreas beta cells, islet cells) they looked at several parameters. Factors considered were peak resolution as a function of matrix type, representative sampling, S/N, effects of rinsing, and retention of spatial distribution. After optimization, scan speed was up (200 shot/sec), and image quality was distinctly improved by such things as omitting pre-scan washes (peptides were too mobile to wait) and tuning the matrix sprayer. As a test of the new protocol, wt and obese (ob/ob) samples were compared.

Minerva, L. et al., Proteomics 2008, 8, 3763–3774.

Candida candidates: Multi-party cell wall congress

Candida albicans is an unpleasant co-resident of our living space. This opportunistic, pathogenic yeast can grow as a blastospore or in a hyphal form with true or pseudohyphae depending on its cell wall. The cell wall is important enough that it gets almost a third of the organismal budget in dry matter. These “funds” are spent on defense, (immuno, scaffolding) and offense (attachment and invasion, logistics, carbohydrates, immunomodulators). Components are classic and unconventional membrane proteins, binding through hydrogen bonds hydrophobic interactions, or covalent links. Castillo et al. give us a thorough description of cell wall components using a combination of 2-DE, MALDI-MS and LC-MS/MS technology and four different fractionation chemistries: HF-saturated pyridine, hot SDS, tryptic digestion, and cold NaOH.

Castillo, L. et al., Proteomics 2008, 8, 3871–3881.

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