Saturday, October 30, 2010

Mass Spectrometry related websites, blogs, etc.

Below, I compiled a list of online resources for mass spectrometry related materials, such as tools, conferences, research blogs, etc. I expect these pointers can keep me and potentially other readers updated if they are frequently visited.

The list may finally appear overwhelming, but enjoy them and make good use of them!

ASMS: (American Society for Mass Spectrometry)

Prof. Murry's Mass Spectrometry blog:

Mass Spectrometry Tools:

Center for Computational MS@UCSD,

MS software on wiki:

BSI PEAKS studio: (commercial one)


MS tutorial video:

Bioinforamtics tools by R. Edgar.
more to come and updated.

If you  find  these stuff useful and informative, or you have some suggestions for improvements, make some constructive comments.

Wednesday, October 20, 2010


ProSightPC 2.0 Software

Thermo Scientific* ProSightPC, the first stand-alone software for analyzing top-down proteomics data, has been enhanced to add support for middle-down and bottom-up experiments, making it an all-around tool for identification and characterization of both intact proteins and peptides.
ProSightPC* 2.0 software enables high-throughput processing of all accurate-mass MS/MS data, whether from top-down, middle-down or bottom-up experiments including the characterization of proteins with known PTMs. ProSightPC 2.0 software uses multiple search modes to determine the exact protein sequence including modifications and alternative splicing. It is the only proteomics software that allows the user to search their tandem MS data against proteome warehouses containing the known biological complexity present in UniProt.

ProSightPC 2.0 software is a complete software package for the identification and characterization of proteins, peptides, and PTMs. It features multiple search modes and can accommodated data generated with several different fragmentation techniques.
Supports top-down, middle-down, and bottom-up experiments
Includes five different search modes, including Accurate Mass, Biomarker, Sequence Tag, Single Protein and Gene Restricted search modes
Processes fragmentation data from ECD, IRMPD or CID

The proprietary ProSight Warehouse includes all known post-translational modifications (PTMs), alternative splicing events and single nucleotide polymorphisms (SNPs)
Import FASTA databases and shotgun annotates these databases with all possible modifications
Includes Sequence Gazer, which allows users to review search results and add, remove, or change modifications to look for better fits

Compatible with:
LTQ FT family of hybrid mass spectrometers
LTQ Orbitrap family of hybrid mass spectrometers
Proteome Discoverer software

A user guide

Monday, October 18, 2010

bioinformatics in China

Bioinformatics in China: A Personal Perspective
Liping Wei and Jun Yu

In this personal perspective, we recall the history of bioinformatics and computational biology in China, review current research and education, and discuss future prospects and challenges. The field of bioinformatics in China has grown significantly in the past decade despite a delayed and patchy start at the end of the 1980s by a few scientists from other disciplines, most noticeably physics and mathematics, where China's traditional strength has been. In the late 1990s and early 2000s, rapid expansion of the field was fueled by the Internet boom and genomics boom worldwide and in China. Today bioinformatics research in China is characterized by a great variety of biological questions addressed and the close collaborative efforts between computational scientists and biologists, with a full spectrum of focuses ranging from database building and algorithm development to hypothesis generation and biological discoveries. Although challenges remain, the future of bioinformatics in China is promising thanks to advances in both computing infrastructure and experimental biology research, a steady increase of governmental funding, and most importantly a critical mass of bioinformatics scientists consisting of not only converts from other disciplines but also formally trained overseas returnees and a new generation of domestically trained bioinformatics Ph.D.s.