Guidelines for the next 10 years of proteomics

Abstract

In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of stringency required in proteomic data generation and analysis appears to have been underestimated. As a result, there are likely to be numerous published findings that are of questionable quality, requiring further confirmation and/or validation. This manuscript outlines a number of key issues in proteomic research, including those associated with experimental design, differential display and biomarker discovery, protein identification and analytical incompleteness. In an effort to set a standard that reflects current thinking on the necessary and desirable characteristics of publishable manuscripts in the field, a minimal set of guidelines for proteomics research is then described. These guidelines will serve as a set of criteria which editors of PROTEOMICS will use for assessment of future submissions to the Journal.

AFM fishing nanotechnology is the way to reverse the Avogadro number in proteomics

“…It may well be that such a practice will help exclude discrepancies in the literature data [2] and, in our opinion, will compel the contributors to adhere to the criteria used by the editors of PROTEOMICS when assessing submissions [3].…”

“…The current situation is perfectly characterized as "we began to run before we could walk" [3]. Although the situation in proteomics has very much in common with the period of implementation of the "Human Genome Project" in 1991-1993, there is a fundamental difference in the proteomic, as opposed to the genomic approach.…”

Proteomic analysis reveals successive aberrations in protein expression from healthy mucosa to invasive head and neck cancer

“…Upon normalization, a further part of the spectra was also eliminated, leaving a total of 303 samples. This study followed criteria from guidelines in publication of peptide and protein identification (Carr et al, 2004;Wilkins et al, 2006).…”

ArMone: A Software Suite Specially Designed for Processing and Analysis of Phosphoproteome Data

“…Researchers may want to report the peptide or protein identifications together with the original mass spectra with matched ions information as part of submission or manuscripts. 16,17 Even though some of the current proteome software suites have modules to show mass spectra with matched ion information for the identified peptides, graphics of the matched spectra are shown one by one. There is currently no publicly available tool for the batch creation of graphics of the matched spectra for all of the identified peptides.…”

“…In addition, the proteomics guideline 16 requires that the identified phosphopeptides/phosphoproteins be accompanied by the annotated and mass labeled spectra for the convenience of other researchers. 16,17 Although some programs can draw the labeled mass spectrum one at a time, the generation of 1000s of images of annotate spectra derived from phosphoproteomic analysis remains a challenge.…”