Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins
Abstract
:1. Introduction
2. Materials and Methods
2.1. neXtProt Data Analysis
2.2. Expression Data Analysis
2.3. Virtual Proteolysis
2.4. Re-Analysis of MS Data
3. Results and Discussion
3.1. “Protein Existence” Features for Human Protein-Coding Genes
3.2. Is the mRNA a Good Helper in Searching for the Missing Proteins?
3.3. MS Detectable or Not?
3.4. Unique Cases—beyond the C-HPP Scope
3.5. One Hit Wonder!
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Category of Biomaterial, Where Gene of Interest Was Observed | Total Number of Genes | Missing Proteins | Uncertain Proteins (PE5) | ||
---|---|---|---|---|---|
PE2 | PE3 | PE4 | |||
All biomaterials | 9542 | 311 | 10 | 6 | 79 |
Part of biomaterials | 3074 | 429 | 41 | 8 | 56 |
Normal or tumor biomaterials * | 161 | 46 | 15 | 0 | 3 |
Only normal | 274 | 55 | 36 | 3 | 4 |
Only cancer | 58 | 12 | 8 | 0 | 4 |
Total | 13,109 | 853 | 110 | 17 | 146 |
# | AC | Gene | Number of Samples | Number of Unique Detectable Tryptic Peptides | ||
---|---|---|---|---|---|---|
Theoretically | Observed in GPMdb | Observed (SRM synt) in PeptideAtlas | ||||
Missing proteins | ||||||
1 | P22532 | SPRR2D | 10 | 1 | 1 | 1/0 |
2 | A0A087WSY6 | IGKV3D-15 | 3 | 1 | 1 | 1/0 |
Uncertain proteins | ||||||
3 | Q58FF3 | HSP90B2P | 1 | 10 | 3 | 1/2 |
4 | Q58FG1 | HSP90AA4P | 1 | 14 | 13 | 7/5 |
5 | Q9BYX7 | POTEKP | 3 | 8 | 8 | 5/5 |
6 | Q9BZK3 | NACA4P | 1 | 5 | 5 | 4/4 |
7 | Q9H853 | TUBA4B | 35 | 9 | 4 | 2/4 |
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Poverennaya, E.; Kiseleva, O.; Ilgisonis, E.; Novikova, S.; Kopylov, A.; Ivanov, Y.; Kononikhin, A.; Gorshkov, M.; Kushlinskii, N.; Archakov, A.; et al. Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. Proteomes 2020, 8, 12. https://doi.org/10.3390/proteomes8020012
Poverennaya E, Kiseleva O, Ilgisonis E, Novikova S, Kopylov A, Ivanov Y, Kononikhin A, Gorshkov M, Kushlinskii N, Archakov A, et al. Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins. Proteomes. 2020; 8(2):12. https://doi.org/10.3390/proteomes8020012
Chicago/Turabian StylePoverennaya, Ekaterina, Olga Kiseleva, Ekaterina Ilgisonis, Svetlana Novikova, Arthur Kopylov, Yuri Ivanov, Alexei Kononikhin, Mikhail Gorshkov, Nikolay Kushlinskii, Alexander Archakov, and et al. 2020. "Is It Possible to Find Needles in a Haystack? Meta-Analysis of 1000+ MS/MS Files Provided by the Russian Proteomic Consortium for Mining Missing Proteins" Proteomes 8, no. 2: 12. https://doi.org/10.3390/proteomes8020012