Proteomics

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A multi-species spike-in sample set for performance evaluation of label-free proteomics quantification

ABSTRACT: When evaluating the quantitative performance of label-free proteomics method(s), samples with known compositions are necessary to define key parameters such as reproducibility, missing data levels, accuracy, precision, as well as sensitivity/specificity for biomarker discovery. Here, we provide a carefully-designed multi-species spike-in sample set for such purposes, which was prepared by spiking small, variable amounts of E. Coli (for mimicking significant protein changes, i.e., true positives) and yeast (for balancing the variable levels of E. coli proteins) proteins into a large, constant background of human proteins (representing unchanged proteins). The sample set encompasses a total of 25 LC-MS sample runs (5 E.coli-level groups, 5 LC-MS replicate runs in each group). The proportion of human proteins is 60% across all samples, and each group contains the following percentage of E. coli and yeast proteins : A: 5%/35%, B: 7.5%/32.5%, C: 10%/30%, D: 15%/25%, E: 20%/20%. These files were used to comprehensively evaluate the quantitative performances by ultra-high-resolution (UHR)-IonStar and SWATH-MS in Result 3.2 of “Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification (DOI: 10.1021/acs.analchem.0c05002)”.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human) Escherichia Coli Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Shuo Qian  

LAB HEAD: Jun Qu

PROVIDER: PXD030780 | Pride | 2022-01-06

REPOSITORIES: Pride

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3Proteome_Human_Yeast_EcoliK12.fasta Fasta
MSGFPlus.jar Other
TechAE_A01.mzXML Mzxml
TechAE_A01.raw Raw
TechAE_A02.mzXML Mzxml
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Publications

Ultra-High-Resolution IonStar Strategy Enhancing Accuracy and Precision of MS1-Based Proteomics and an Extensive Comparison with State-of-the-Art SWATH-MS in Large-Cohort Quantification.

Wang Xue X   Jin Liang L   Hu Chenqi C   Shen Shichen S   Qian Shuo S   Ma Min M   Zhu Xiaoyu X   Li Fengzhi F   Wang Jianmin J   Tian Yu Y   Qu Jun J  

Analytical chemistry 20210309 11

Quantitative proteomics in large cohorts is highly valuable for clinical/pharmaceutical investigations but often suffers from severely compromised reliability, accuracy, and reproducibility. Here, we describe an ultra-high-resolution IonStar method achieving reproducible protein measurement in large cohorts while minimizing the ratio compression problem, by taking advantage of the exceptional selectivity of ultra-high-resolution (UHR)-MS1 detection (240k_FWHM@<i>m</i>/<i>z</i> = 200). Using mixe  ...[more]

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