Automated Data Extraction from In Situ Protein-Stable Isotope Probing Studies

Abstract

Protein-stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism(s), a key application will be in situ studies of microbial communities for short periods of time under natural conditions that result in small degrees of partial labeling. One hurdle restricting large-scale in situ protein-SIP studies is the lack of algorithms and software for automated data processing of the massive data sets resulting from such studies. In response, we developed Stable Isotope Probing Protein Extraction Resources software (SIPPER) and applied it for large-scale extraction and visualization of data from short-term (3 h) protein-SIP experiments performed in situ on phototrophic bacterial mats isolated from Yellowstone National Park. Several metrics incorporated into the software allow it to support exhaustive analysis of the complex composite isotopic envelope observed as a result of low amounts of partial label incorporation. SIPPER also enables the detection of labeled molecular species without the need for any prior identification.

Proteomic Stable Isotope Probing Reveals Taxonomically Distinct Patterns in Amino Acid Assimilation by Coastal Marine Bacterioplankton

“…The protein-SIP approach produces detailed quantification of label incorporation into a defined set of identified proteins. First, unlabeled peptides are identified by tandem mass spectrometry (MS/MS), and then isotope incorporation into a predefined set of peptides is characterized through manual examination of mass spectra from coeluted isotopologues ( 40 – 44 ). The proteomic stable isotope probing (proteomic SIP) technique ( 45 ) used in this study expands on current metaproteomic approaches ( 46 – 48 ) by providing detailed information on stable isotope enrichment patterns for a wide diversity of peptides, in addition to identifying and quantifying thousands of unlabeled microbial proteins.…”

Endoscopic removal of bullets from the cranial ridge junction region via transoral and transnasal approaches

“…Thus, Slysz et al had recently recommended that surgical removal of the bullets is necessary. [3] Given that the approach of lateral neck incision for bullet removal may markedly increase the likelihood of neurovascular injury, [4,5] surgical management of the gunshot wounds of the spine is not widely advocated, and microscopic techniques may be a good strategy for removal of the foreign bodies in the cervical spine. [6] …”

MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics

“…Therefore, it 23 can be assumed that iFPR estimation is conservative and in this example below 1.5% at a peptide identification FDR of 2%. As control experiment the 12 We could demonstrate that the isotope incorporation can be detected and quantified reproducibly at the level of relative isotope abundance. Similarly, the labeling ratio can be determined, which is a measure for induction and protein turnover.…”