蛋白组文献

The protein landscape of chronic lymphocytic leukemia

blood的文献

Details on the Spectronaut settings are provided in supplemental Methods. The Spectronaut reports were exported and further processed in R (version 3.6.0). Normalization, quality control and transformation of raw protein abundance data were done with the R/Bioconductor package DEP.16 Proteins were selected for analysis if they showed <50% missing values across patient samples. The 50% cutoff choice follows similar previous studies.17-19 The protein abundance data were background corrected, scaled, and transformed using the variance stabilizing transformation approach of Huber et al and Karp et al.20,21

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938101/
vsn和稳定性的

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8294761/
相关进展 生信分析系列干货 | 高分文章蛋白质组学数据预处理方法调研报告
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9869594/ DEP包分析

ingle-nucleus RNA sequencing and deep tissue proteomics reveal distinct tumour microenvironment in stage-I and II cervical cancer 一般定量
https://www.jthjournal.org/article/S1538-7836(22)01808-6/fulltext#secst0065 提到用到了这个包
MSstats: an R package for statistical analysis of quantitative mass spectrometry‐based proteomic
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9375823/

1. 蛋白搜库

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9967398/

Protein quantification was subsequently carried out using the MaxLFQ algorithm implemented in DIA-NN. The intensity values were log2-transformed for calculation and statistical analysis. For data filtration, a strict filtering rule was set as that, only proteins detected simultaneously in all GBM and peritumoral specimens were retained for quantification. Next, the quantification matrix was subjected to a global median normalization to normalize out the technical differences.

搜狗推文 蛋白质组学上游数据处理知多少

Nat Commun|DIA 蛋白质组学和磷酸化蛋白质组学常用软件和分析工作流程的基准测试

zhanghanqing 靶标发现与药物研发 2023-06-07 08:03

大家好，今天给大家分享一篇2023年1月发表在Nature Communications上题目“Benchmarking commonly used software suites and analysis workflows for DIA proteomics and phosphoproteomics”的研究论文。文章的通讯作者是来自上海科技大学的水雯箐研究员，水雯箐课题组致力于运用生物质谱、蛋白质组学、生物信息学等手段进行新型配体发现与新药物靶点的挖掘。

研究人员建立了 DIA 基准数据集，模拟复杂背景下数千种蛋白质的调节，在 Orbitrap 和 timsTOF 上采集。通过分析蛋白质组学数据以及磷酸化蛋白质组学数据，评估了四种常用的 DIA 软件（DIA-NN、Spectronaut、MaxDIA 和 Skyline）。研究结果提示 DIA-NN 和 Spectronaut 在分析DIA 蛋白质组学数据方面具有独特优势。

差异分析评价

Nature method

High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells | Nature Communications

搜库

Only peptides with average reporter signal-to-noise >3 were used, and phosphorylation localisation probabilities were estimated with the IMP-ptmRS node.

1. 蛋白的 ratio，是由该蛋白所有肽段的 SILAC ratio 的中位数得到。
2. 原因：中位数能抵抗极端值，比平均值更可靠。
   1. 所以蛋白 ratio 不是加权平均，而是取所有肽段 ratio 的中位数。
   2. 因为中位数是稳健统计量，所以少数异常肽段不会影响蛋白 ratio。

那么 “normalized SILAC pair ratio” 怎么做？

在 MaxQuant / SILAC 中通常：

1. 对所有 peptide ratio 的 log2 值做 全局中位数归一化 或者依赖 MaxQuant 的 built-in normalization（Ratio normalized column）