Stem-cell scientist found guilty of misconduct
But Japanese researcher stands by her claim to be able to produce stem cells using an acid bath or mechanical stress.
Suicide notes of Yoshiki Sasai
Japanese stem cell scientist Yoshiki Sasai committed suicide two weeks ago. He left few suicide notes, one of which was addressed to Haruko Obakata (the author of STAP papers) and released for public right after tragedy. It said: “Be sure to reproduce STAP cells”. This week, more Sasai’s suicide notes were released to public:The lawyer, Kazuhiro Nakamura, released a brief summary of the two notes left for family members. In them, Dr. Sasai apologized for leaving them behind and said “unfair bashing” by the media and his responsibilities at his laboratory and Riken left him exhausted, according to the lawyer.
Btw, detailed STAP protocol, released in March by RIKEN is now retracted.
One side of whole STAP story was poorly discussed in media and among scientists – the role of Nature magazine. Some of us, including myself, thought that publisher (namely Nature Publishing Group) should make a decision to release STAP papers peer reviewers comments and editorial correspondence. We believed that it will benefit the process of scientific publishing and science in general by learning from mistakes.
Retraction: clinical and technical phosphoproteomic research
This article [1] has been regretfully retracted by the Editors because of significant overlap with a figure and text from previously published articles [2-4]. We apologise to all affected parties for the inconvenience caused.
Guidelines for the next 10 years of proteomics
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.
Controlled vocabularies and ontologies in proteomics: Overview, principles and practice
This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the “mapping files” used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era.
The Work of the Human Proteome Organisation’s
Proteomics Standards Initiative (HUPO PSI)
CHRIS F. TAYLOR, HENNING HERMJAKOB, RANDALL K. JULIAN, JR.,
JOHN S. GARAVELLI, RUEDI AEBERSOLD, and ROLF APWEILER
This article describes the origins, working practices and various development projects of the
HUman Proteome Organisation’s Proteomics Standards Initiative (HUPO PSI), specifically,
our work on reporting requirements, data exchange formats and controlled vocabulary
terms. We also offer our view of the two functional genomics projects in which the PSI plays
a role (FuGE and FuGO), discussing their impact on our process and laying out the benefits
we see as accruing, both to the PSI and to biomedical science as a whole as a result of
their widespread acceptance.
This paper is part of the special issue of OMICS on data standards.
Guidelines for reporting quantitative mass spectrometry based experiments in proteomics
Salvador Martínez-Bartolomé et al.
Mass spectrometry is already a well-established protein identification tool and recent
methodological and technological developments have also made possible the extraction of
quantitative data of protein abundance in large-scale studies. Several strategies for absolute
and relative quantitative proteomics and the statistical assessment of quantifications are
possible, each having specific measurements and therefore, different data analysis workflows.
The guidelines for Mass Spectrometry Quantification allow the description of a wide range
of quantitative approaches, including labeled and label-free techniques and also targeted
approaches such as Selected Reaction Monitoring (SRM).
Biological significance
The HUPO Proteomics Standards Initiative (HUPO-PSI) has invested considerable efforts to
improve the standardization of proteomics data handling, representation and sharing
through the development of data standards, reporting guidelines, controlled vocabularies and tooling. In this manuscript, we describe a key output from the HUPO-PSI—namely the
MIAPE Quant guidelines, which have developed in parallel with the corresponding data
exchange format mzQuantML [1]. The MIAPE Quant guidelines describe the HUPO-PSI
proposal concerning the minimum information to be reported when a quantitative data set,
derived from mass spectrometry (MS), is submitted to a database or as supplementary
information to a journal. The guidelines have been developed with input from a broad
spectrum of stakeholders in the proteomics field to represent a true consensus view of the
most important data types and metadata, required for a quantitative experiment to be
analyzed critically or a data analysis pipeline to be reproduced. It is anticipated that they will
influence or be directly adopted as part of journal guidelines for publication and by public
proteomics databases and thus may have an impact on proteomics laboratories across the
world. This article is part of a Special Issue entitled: Standardization and Quality Control.
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