Project description:Mass spectrometry (MS)-based proteomics is known for its high accuracy in quantifying peptides and proteins using various calibration strategies, including internal and external calibration curves. While external multi-point calibration curves are created from serial dilutions, they often fail to account for sample-specific matrix effects. In contrast, internal calibration curves account for sample matrix but face scalability and cost challenges for whole proteome analyses. In this manuscript we present a novel TMT-based multipoint internal calibration curve strategy, referred to as TMTCal, which enables the generation of internal calibration curves for all peptides identified within a proteome within a single experiment. We applied this strategy to human ovarian cancer cells to evaluate the linear quantitative responses of all the identified peptides and reveal the significant proteome changes associated with cisplatin treatment.
Project description:We evaluated quantification using XLE by testing 68 different chemicals (PCB, PBDEs, chlorinated pesticides) in SRM-1958 using external calibration curves (0.05 to 2 ng/mL) and comparing measured values to the reference concentrations reported for SRM. We identified all 40 PCBs that are reported with a reference mass fraction (including certified values and non-certified estimates) in the range of 46.6 to 490 ng/kg in SRM-1958 certificate of analysis (issue date: 11 October 2018). Quantification without adjustment for recovery was reproducible with 29 PCB qualifications at >70% and 35 PCBs at >65% of the reference levels. Eleven out of 13 PBDE/PBBs and all 17 organochlorine pesticides were identifiable and reproducibly quantified in this experiment. Therefore, XLE provides sufficient recovery to support accurate absolute quantification of a broad range of environmental chemicals. Overall, XLE supported measurement of 68 out of the 70 chemicals that are in the ng/kg range in SRM-1958.
Project description:20 random DNA barcodes were designed in silico and transfected into PC3 cells. Barcodes were sequenced using Illumina-Miseq technology to find the sequence and their respective copy numbers. Current file contains the raw data of these DNA barcodes in fastq format