Protein Quantitation

Typical challenges in non-targeted protein quantitation are the cycle time (defining the chromatographic peak resolution), the uniqueness of the ion(s) chosen to determine a peptide amount (selectivity) and the system sensitivity (quantitation of low-abundance compounds). MS-based approaches provide comprehensive quantitative results but overlapping ions reduce the selectivity of these workflows. MS/MS (DIA) based quantitation provides excellent selectivity at the cost of reduced sensitivity.

Tims-Pasef^®基于无标签的定量（Pasef^®-lfq）结合了两种方法中最好的。TIMS既提供了分离的额外维度，也提供了大大提高选择性，而Tims细胞的预浓缩效应提供了更大的灵敏度。Pasef^®与传统的DDA方法相比，周期时间与狭窄的纳米-UHPLC峰兼容，而其速度（> 100 Hz MS/MS）极大地提高了父离子选择的可重复性。
In this case, the timsTOF Pro’s unique 4D-MBR approach allows to overcome the missing value problem with an unprecedented sensitivity.

In some cases, highly complex samples or short gradient analysis, the 100 Hz MS/MS repletion rate is not sufficient to reproducibly select the same ions over a large set of analyses

在这种情况下可再生的碰撞十字交会tion determination (mobility) enables 4D-Match Between Runs (MBR) which maximizes the number of proteins quantified from Label Free Quantification experiments while maintaining the highest level of confidence for high throughput sample analysis. The 4D-MBR approach is supported by the latest PEAKS and MaxQuant versions. Read our correspondingLC-MS154申请注释.

踏入未来：引入Dia-Pasef^®
For data independent acquisition (DIA), dia-PASEF^®leverages the correlation between molecular mass and mobility to target the densest peptide region. The extra dimension results in increased selectivity, increased sensitivity and shorter cycle times. For more information on how dia-PASEF^®pushes the limits of 4D-Proteomics™, read ourLC-MS157 application note.

最大数据处理
MaxQuant, the popular, powerful, open-source software fully supports PASEF^®-LFQ数据启用高级定量，可视化和报告。

高级软件支持
现在，越来越多的高级蛋白质组学处理软件包直接读取原始数据：这包括天际线，基因数据，完整的蛋白质指标套件，吉祥物蒸馏器

PEAKS data processing
PEAKS Studio is powered by high performance feature extraction from tims data files, obtaining high quality results in peptide-based protein identification, label-free quantitation and DeNovo sequencing. Multiple sophisticated visualization and exporting capacities allow users to review, share or refine results from multiple proteomics analyses.

The unique ability of the timsTOF Pro to deliver sustainable performance over thousands of injections combined with the enhanced LFQ performance make the system an ideal platform for high-throughput clinical research.

Data processing is key for protein quantitation and the PASEF^®-LFQ approach is already supported by some of the most powerful software suites.