In the era of studies of increasing complexity, availability of high-resolution mass spectrometers, and large datasets generated by these experimental workflows, the need for scalable and accurate computational methods is more urgent than ever. In response to this need, this special issue of JPR will collect:
reviews of the state of the art in large-scale computational mass spectrometry,
opinion pieces related to computational and statistical issues in mass spectrometric and integrative investigations
manuscripts describing new methods in the areas of algorithms, statistics and machine learning
manuscripts introducing new tools (software, databases, web servers), or improvements upon the existing tools, for large-scale analysis, and case studies exemplifying best practices in large-scale investigation.
Encouraged topics include (but are not limited to):
Combined large-scale experimentation and computation
Computational methods for emerging high-throughput technologies (e.g., single-cell technologies, spatial omics, MS imaging)
Novel approaches to studies of genomic variants produced by alternative splicing (AST) and coding non synonymous single nucleotide polymorphisms (cSNPs).
Analysis of heterogeneous populations (e.g., heterogeneous biological groups, cell populations)
Personalized omics and personalized biomarker detection
Statistical inference on large-scale datasets and multi-omics datasets
Integrative analysis of multiple omics technologies (including but not limited to genomics, transcriptomics, proteomics, metabolomics)
Integration across scales (multiple temporal and spatial resolutions)
Statistical assessment of confidence in identified and quantified peptides, protein groups, and individual protein species
Novel approaches to characterize absent or low-abundant analytes
Scalability and reproducibility
Repeatability and reproducibility of large-scale computational research
Best practices for data exchange, deposition, and processing
Grid computing, cloud computing, and scientific workflows
Re-analysis of datasets available in comprehensive repositories
Submission Deadline: September 14, 2015
Large-scale Computational Mass Spectrometry and Multi-omics
Guest Editors Olga Vitek Northeastern University
Oliver Kohlbacher University of Tübingen
Co-Editors William S. Hancock Northeastern University
Susan Weintraub The University of Texas Health Science Center at San Antonio
SUBMISSION PROCEDURE Manuscripts must be submitted by September 14, 2015 to be considered for this Special Issue. Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system. Prospective authors should prepare manuscripts according to the JPR guidelines for submission.
Authors should indicate in the Comments to the Editor that the
manuscript is submitted for publication in the Special Issue: Large-scale computational mass spectrometry and multi-omics. Where applicable, raw data and metadata must be deposited via ProteomeXchange, with the PXD identifier in the final sentence of the Abstract. The target final acceptance date is November 2, 2015.
REVIEW AND PUBLICATION PROCESS All
submitted manuscripts will be subject to initial editorial review to
determine whether they are appropriate for the Special Issue. Those not
meeting this criterion may be considered for a regular issue of the
journal or returned. All relevant papers will go through full peer
review. Due to the publication schedule, only papers requiring no or
minor revision will be accepted for this Special Issue. Papers requiring
major revision may be considered for later regular issues.