Label-free peptide profiling of Orbitrap™ full mass spectra

Background. We developed a new version of the open source software package Peptrix that can yet compare large numbers of Orbitrap™ LC-MS data. The peptide profiling results for Peptrix on MS1 spectra were compared with those obtained from a small selection of open source and commercial software packages: msInspect, Sieve™ and Progenesis™. The properties compared in these packages were speed, total number of detected masses, redundancy of masses, reproducibility in numbers and CV of intensity, overlap of masses, and differences in peptide peak intensities. Reproducibility measurements were taken for the different MS1 software applications by measuring in triplicate a complex peptide mixture of immunoglobulin on the Orbitrap™ mass spectrometer. Values of peptide masses detected from the high intensity peaks of the MS1 spectra by peptide profiling were verified with values of the MS2 fragmented and sequenced masses that resulted in protein identifications with a significant score. Findings. Peptrix finds about the same number of peptide features as the other packages, but peptide masses are in some cases approximately 5 to 10 times less redundant present in the peptide profile matrix. The Peptrix profile matrix displays the largest overlap when comparing the number of masses in a pair between two software applications. The overlap of peptide masses between software packages of low intensity peaks in the spectra is remarkably low with about 50% of the detected masses in the individual packages. Peptrix does not differ from the other packages in detecting 96% of the masses that relate to highly abundant sequenced proteins. MS1 peak intensities vary between the applications in a non linear way as they are not processed using the same method. Conclusions. Peptrix is capable of peptide profiling using Orbitrap™ files and finding differential expressed peptides in body fluid and tissue samples. The number of peptide masses detected in Orbitrap™ files can be increased by using more MS1 peptide profiling applications, including Peptrix, since it appears from the comparison of Peptrix with the other applications that all software packages have likely a high false negative rate of low intensity peptide peaks (missing peptides)

Truncating the i-leader open reading frame enhances release of human adenovirus type 5 in glioma cells

Background: The survival of glioma patients with the current treatments is poor. Early clinical trails with replicating adenoviruses demonstrated the feasibility and safety of the use of adenoviruses as oncolytic agents. Antitumor efficacy has been moderate due to inefficient virus replication and spread. Previous studies have shown that truncation of the adenovirus i-leader open reading frame enhanced cytopathic activity of HAdV-5 in several tumor cell lines. Here we report the effect of an i-leader mutation on the cytopathic activity in glioma cell lines and in primary high-grade glioma

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-4

<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-2

1154.7128 Da, represented by the grey lines, is as expected not present in Glioma vessels.<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p

A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation-0

Ioma vessels with codes TH1 to TH10, 10 spectra of normal vessels with codes S1 to S10, and 10 spectra of tissue surrounding the normal vessels with codes TS1 to TS10 are included. Two "normal vessels" samples, S5 and TS5, were excluded because they could not be calibrated. The highlighted box in Figure 3 represents the hierarchical clustering order 490 with mass 1037.5355 Da to 789 with mass 1665.7891 Da as presented (see Additional file ).<p><b>Copyright information:</b></p><p>Taken from "A software application for comparing large numbers of high resolution MALDI-FTICR MS spectra demonstrated by searching candidate biomarkers for glioma blood vessel formation"</p><p>http://www.biomedcentral.com/1471-2105/9/133</p><p>BMC Bioinformatics 2008;9():133-133.</p><p>Published online 1 Mar 2008</p><p>PMCID:PMC2323386.</p><p></p