Showing posts with label LC-MS/MS. Show all posts
Showing posts with label LC-MS/MS. Show all posts

Thursday, 23 October 2014

Which journals release more public proteomics data!!!

I'm a big fan of data and the -omics family. Also, I like the idea of make more & more our data public available for others, not only for reuse, but also to guarantee the reproducibility and quality assessment of the results (Making proteomics data accessible and reusable: Current state of proteomics databases and repositories). I'm wondering which of these journals (list - http://scholar.google.co.uk/) encourages their submitters and authors to make their data publicly available:



Journal
h5-index
h5-median
Molecular & Cellular Proteomics
74
101
Journal of Proteome Research
70
91
Proteomics
60
76
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics
52
78
Journal of Proteomics
49
60
Proteomics - Clinical Applications
35
43
Proteome Science
23
32

After a simple statistic, based on PRIDE data:


Number of PRIDE projects by Journal

Monday, 8 September 2014

Evaluation of Proteomic Search Engines for PTMs Identification

The peptide-centric MS strategy is called bottom-up, in which proteins are extracted from cells, digested into peptides with proteases, and analyzed by liquid chromatography tandem mass spectrometry (LC−MS/MS). More specifically, peptides are resolved by chromatography, ionized in mass spectrometers, and scanned to obtain full MS spectra. Next, some high-abundance peptides (precursor ions) are selected and fragmented to obtain MS/MS spectra by high- energy C-trap dissociation (HCD) or collision-induced dissociation (CID). 

Then, peptides are commonly identified by searching the MS/MS spectra against a database and finally assembled into identified proteins. Database searching plays an important role in proteomics analysis because it can be used to translate thousands of MS/MS spectra into protein identifications (IDs). 

Many database search engines have been developed to quickly and accurately analyze large volumes of proteomics data. Some of the more well-known search engines are MascotSEQUEST, PEAKS DB, ProteinPilot, Andromeda, and X!Tandem. Here a list of commonly use search engines in proteomics and mass spectrometry.