User guide:
1. This database includes mass spectrometry–based proteomics data from 568 patient-derived xenograft (PDX) models across 25 cancer types. To minimize interference from mouse stromal proteins commonly present in PDX samples, we applied a separate-then-run strategy, in which mouse stromal cells were removed prior to MS acquisition [1]. Proteomic profiling was primarily performed on the Astral platform, and protein expression levels were represented by ion intensities, which were quantified and normalized using the MaxLFQ algorithm.

2. Users can search for the expression of a specific protein by entering its corresponding gene symbol. The results include a bar plot showing relative protein abundance across selected models, along with a table summarizing protein group (PG) information, PG expression values, and molecular weights (in Daltons).

A protein group refers to one or more proteins identified based on the same set of peptides. Each group is reported using UniProt accession numbers, separated by semicolons if multiple proteins are present. For example, querying the gene symbol “CCZ1” returns a protein group containing two proteins (P86790 and P86791). These proteins share high sequence similarity, which leads to ambiguity in distinguishing their individual expression levels. Notably, more than 99% of protein groups in this database correspond to a single unique protein.

3. To evaluate a protein’s expression level in the context of the entire dataset, the database automatically displays a static Comparative Distribution figure for each gene. The figure appears below the scatter plot and summarizes the target’s proteomic expression (and transcriptomic expression, where available) relative to all models in the database. This visualization places the selected protein and its corresponding gene within the global expression landscape, helping users determine whether the target is relatively high or low in expression.

4. In some cases, different models may be assigned different protein groups for the same gene. This can result from experimental variation (e.g., models analyzed in different batches) or isoform-related differences. As such, models with different protein groups should not be directly compared, as their expression values are not interchangeable. For example, when querying the gene “ATP5F1E”, two distinct protein groups may appear: one as “P56381” and the other as “P56381;Q5VTU8”. These represent different sets of identified peptides, and their expression values are not comparable. To assist users, the bar plot visually groups and color-codes models by their corresponding protein group.

Reference:
[1] Zhaomei Shi, Binchen Mao, Xiaobo Chen, Piliang Hao, Sheng Guo; Mouse Stromal Cells Confound Proteomic Characterization and Quantification of Xenograft Models. Cancer Research Communications 1 February 2023; 3 (2): 202–214. https://doi.org/10.1158/2767-9764.CRC-22-0431

Disclaimer:
CROWN BIOSCIENCE DOES NOT MAKES ANY REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, AND EXPRESSLY DISCLAIMS ALL IMPLIED WARRANTIES OF TITLE, NON-INFRINGMENT, MERCHANTIBILITY, AND FITNESS FOR A PARTICULAR PURPOSE OF THIS DATABASE.