# Protein expression data

**URL:** <https://forum.depmap.org/t/protein-expression-data/1065>\
**Category:** Q&A\
**Created:** [December 7, 2021, 11:47am UTC](https://forum.depmap.org/t/protein-expression-data/1065 "2021-12-07T11:47:38Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Nancy.alnassar](https://avatars.discourse-cdn.com/v4/letter/n/f475e1/32.png) [@Nancy.alnassar](https://forum.depmap.org/u/Nancy.alnassar)\
**Post date:** [December 7, 2021, 11:47am UTC](https://forum.depmap.org/t/protein-expression-data/1065/1 "2021-12-07T11:47:38Z")

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Hello! I have a question regarding the proteomics dataset. I read that the protein quantitative profiling by MS was conducted in 375 cell lines. However, when I looked at the expression of some proteins, I only found results in a small number of cell lines (for examples 18 cell lines). Does this mean that the these proteins have an expression value of 0 in all other cell lines that were used for the MS profiling? Or does it mean something else?  
Thanks!

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**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [December 7, 2021, 3:50pm UTC](https://forum.depmap.org/t/protein-expression-data/1065/2 "2021-12-07T15:50:54Z")

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Hi. Could you please point me to the file that you are looking at?

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**Author:** ![Nancy.alnassar](https://avatars.discourse-cdn.com/v4/letter/n/f475e1/32.png) [@Nancy.alnassar](https://forum.depmap.org/u/Nancy.alnassar)\
**Post date:** [December 8, 2021, 2:06pm UTC](https://forum.depmap.org/t/protein-expression-data/1065/3 "2021-12-08T14:06:45Z")

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Sure. When I use the Data Explorer and choose the Proteomics dataset to look at the expression of the protein encoded by MYOD1 for example, I get the protein expression values in 18 cell lines. However, when I look at the protein encoded by SNTB2, I get results for 375 cell lines.  
Does this mean that MYOD1 was only found to be expressed in 18 cell lines, or that the expression of MYOD1 was only quantified in those 18 cell lines?

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**Author:** ![jnoorbak](https://yyz1.discourse-cdn.com/flex035/user_avatar/forum.depmap.org/jnoorbak/32/12_2.png) [@jnoorbak](https://forum.depmap.org/u/jnoorbak)\
**Post date:** [December 8, 2021, 9:43pm UTC](https://forum.depmap.org/t/protein-expression-data/1065/4 "2021-12-08T21:43:01Z")

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Hi, the masspec data has many NAs in it. I checked these two lines specifically and what you’re describing matches the missing values in our dataset.

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**Author:** ![Nancy.alnassar](https://avatars.discourse-cdn.com/v4/letter/n/f475e1/32.png) [@Nancy.alnassar](https://forum.depmap.org/u/Nancy.alnassar)\
**Post date:** [December 8, 2021, 10:22pm UTC](https://forum.depmap.org/t/protein-expression-data/1065/5 "2021-12-08T22:22:52Z")

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I see. thanks very much for your help!