Data set of the week: (2014/3/5)
Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology.
Overall rating: very good data (specialist interest)
This data set consisted of 1 result, obtained from a single LC/MS/MS analysis. The data files were made available through ProteomeXchange, PXD000460. It has been published by Legendre M, Bartoli J, Shmakova L, Jeudy S, Labadie K, Adrait A, Lescot M, Poirot O, Bertaux L, Bruley C, Couté Y, Rivkina E, Abergel C and Claverie JM, Proc Natl Acad Sci U S A. 2014 Mar 3 (PubMed).
This study involves the characterization of the giant virus Pithovirus sibericum, a 1.5 micron long amphora-shaped viron. The virus was isolated from a 30,000 year old sediment and grown in Acanthamoeba castellanii. The virus has a 600 kilobase genome, with open reading frames for approximately 2,500 proteins. The proteomics study made available was obtained from isolated viron particles, with 70 identified proteins from the host A. castellanii and 193 proteins from P. sibericum. While the peptides showed a considerable amount of non-tryptic cleavage, the mass spectrometry and chromatography were both very well done.
Changing the naming convention for amino acid polymorphisms (2014/2/4)
GPM and GPMDB have been acquiring information about amino acid polymorphisms since the system began operating in 2004. The process accelerated sigificantly with the introduction of dbSNP annotation information in 2006. Nucleotide polymorphism research has advanced tremendously during this period, to the point that the original term "polymorphism" no longer accurately describes the phenomena being studied. The term SNP has been largely replaced by SNV (Single Nucleotide Variant) to reflect the changes in the field. To keep up with these changes, GPM and GPMDB will be altering all references to SNPs and SNAPs (Single Nucleotide-induced Amino acid Polymorphisms) to SNVs and SAVs (Single Amino acid Variants). The name of the server used to provide the interface for GPMDB's collected SAV information with remain stable at snap.thegpm.org, but the alias sav.thegpm.org will be added for forward compatibility.
System updates for GPMDB's 10th anniversary (2014/2/4)
GPMDB had its tenth anniversary of operation on Jan. 1, 2014: the public interface was first made available on Jan. 1, 2004. The overall success of the project has made it necessary to invest in updating the hardware and software resource that run GPMDB on a daily basis. Today marks the end of this upgrade cycle, with the successful completion of adding a new, faster server for processing incoming data files into database entries. The following items have been added/upgrading during the process:
Data set of the week: (2014/2/2)
Glomerular Cell Cross-Talk Influences Composition and Assembly of Extracellular Matrix.
Overall rating: very good data (specialist interest)
This data set consisted of 180 results, each an LC/MS/MS analysis of an SDS-PAGE gel band. The data files were made available through ProteomeXchange, PXD000643. It has been published by Byron A, Randles MJ, Humphries JD, Mironov A, Hamidi H, Harris S, Mathieson PW, Saleem MA, Satchell SS, Zent R, Humphries MJ, and Lennon R, J Am Soc Nephrol. 2014 Jan 16 (PubMed).
This study focussed on an often ignored tissue compartment: the clumsily-named "extracellular matrix". While this essential component of tissue varies widely in protein composition and it is essential for organ function, the proteomics community has spent comparatively little effort characterizing the associated tissue-specific proteomes. The data reported in this manuscript uses standard methods to investigate the proteins of glomerular extracellular matrix, providing a good insight into its composition.
Data set of the week: (2014/1/26)
Proteomic analysis of purified protein derivative of Mycobacterium tuberculosis.
Overall rating: very good data (general interest)
This data set consisted of 1 result, a single injection LC/MS/MS experiment. The data file was made available through ProteomeXchange, PXD000377. It has been published by Prasad TS, Verma R, Kumar S, Nirujogi RS, Sathe GJ, Madugundu AK, Sharma J, Puttamallesh VN, Ganjiwale A, Myneedu VP, Chatterjee A, Pandey A, Harsha H, and Narayana J, Clin Proteomics. 2013 Jul 19;10(1):8 (PubMed).
While many published 'omics studies focus on the heroic collection of large volumes of data, this study is more of a haiku: a quiet reflection on an important clinical material. By limiting the study to simply looking at the real composition of "Purified Protein Derivative" (the antigenic material used for the tuberulosus skin test), the authors clearly demonstrate both the power of the now-routine techniques employed and beg the question of why this type of analysis is not available for every batch of this product used clinically.
Data set of the week: (2014/1/19)
Comparative Proteome Analysis Revealing an 11-Protein Signature for Aggressive Triple-Negative Breast Cancer.
Overall rating: excellent data (leading the field)
This data set consisted of 126 results, each one a 3 hour gradient LC/MS/MS experiment from laser microdisected samples. The data files were made available through PeptideAtlas, PASS00260. It has been published by Liu NQ, Stingl C, Look MP, Smid M, Braakman RB, De Marchi T, Sieuwerts AM, Span PN, Sweep FC, Linderholm BK, Mangia A, Paradiso A, Dirix LY, Van Laere SJ, Luider TM, Martens JW, Foekens JA and Umar A, J Natl Cancer Inst. 2014 Jan 7 (PubMed).
This study represents probably the best clinical proteomics data set obtained from laser microdisection samples. The starting material used in each analysis was approximately 4,000 human breast cancer epithelial cells removed from frozen tissue samples. The resulting set of spectra and identifications were surprisingly consistent, producing very few experimental artifacts as well as excellent reproducibility of the HPLC-MS profiles and peptide identifications. Any group interesting in trying to find rare post-translational modifications, single amino acid variants or simply understanding the limits of reproducibililty in this type of experiment should consider using this data set.
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