PeptideAtlas

[…] 1. RNA-seq datasets have been deposited in ENA; accession number PRJEB23469.2. SWATH MS data and OpenSWATH outputs have been deposited in PeptideAtlas under identifier PASS00685 (http://www.peptideatlas.org/PASS/PASS00685).The Mycobacterium tuberculosis complex (MTBC) includes the most important global pathogens for humans and animals, […]

[…] C-HPP, the work of the proteome inventory was split among different teams and countries [].At the beginning of the C-HPP there were established resources on proteomic MS-data (PRIDE [], GPMdb [] and PeptideAtlas []); affinity data (Human Protein Atlas []); human proteome data in neXtProt []; and flexible platforms to work with heterogeneous molecular data, such as TAVERNA []. Despite such a repre […]

[…] bove presented results, the LC-MS data sets of the 24 serum samples were also searched against differentially sized custom glycoprotein databases created from (i) all known plasma/serum proteins from PeptideAtlas build 2010 (2421 glycoproteins), (ii) all deamidated proteins identified following PNGaseF treatment of glycopeptides from the same 24 serum samples (280 glycoproteins) and (iii) Swiss-Pr […]

[…] reliability of the MS result, all succinylation sites identified at the C-terminal were removed before the bioinformatics analysis. All raw data have been uploaded to the publicly accessible database PeptideAtlas (data set ID PASS00795) (http://www.peptideatlas.org/PASS/PASS00795) (, ). […]

[…] de AVNGFLADLFTK; m/z 648.3533, collision energy of 26, and an isolation width of 4. Data was analysed using the open source software Skyline where it was compared to a DEPD5 spectral library acquired PeptideAtlas (http://www.peptideatlas.org/speclib/). The following Skyline settings were used; trypsin digestion, no missed trypsin cleavages, variable modifications of carbamidomethyl and oxidation, […]

[…] er sample in which design these experiments can be guided by the combination of the proteomic and transcriptomic experiments performed in this study.Additionally, the information on resources such as PeptideAtlas and SRM Atlas could help prioritizing missing proteins for further validation. From the 165 one-hit wonder proteins identified in our analysis, we have found other additional unique pepti […]