TY - JOUR
T1 - Crystal-C
T2 - A Computational Tool for Refinement of Open Search Results
AU - Chang, Hui Yin
AU - Kong, Andy T.
AU - Da Veiga Leprevost, Felipe
AU - Avtonomov, Dmitry M.
AU - Haynes, Sarah E.
AU - Nesvizhskii, Alexey I.
AU - Nesvizhskii, Alexey I.
N1 - Publisher Copyright:
Copyright © 2020 American Chemical Society.
PY - 2020/6/5
Y1 - 2020/6/5
N2 - Shotgun proteomics using liquid chromatography coupled to mass spectrometry (LC-MS) is commonly used to identify peptides containing post-translational modifications. With the emergence of fast database search tools such as MSFragger, the approach of enlarging precursor mass tolerances during the search (termed "open search") has been increasingly used for comprehensive characterization of post-translational and chemical modifications of protein samples. However, not all mass shifts detected using the open search strategy represent true modifications, as artifacts exist from sources such as unaccounted missed cleavages or peptide co-fragmentation (chimeric MS/MS spectra). Here, we present Crystal-C, a computational tool that detects and removes such artifacts from open search results. Our analysis using Crystal-C shows that, in a typical shotgun proteomics data set, the number of such observations is relatively small. Nevertheless, removing these artifacts helps to simplify the interpretation of the mass shift histograms, which in turn should improve the ability of open search-based tools to detect potentially interesting mass shifts for follow-up investigation.
AB - Shotgun proteomics using liquid chromatography coupled to mass spectrometry (LC-MS) is commonly used to identify peptides containing post-translational modifications. With the emergence of fast database search tools such as MSFragger, the approach of enlarging precursor mass tolerances during the search (termed "open search") has been increasingly used for comprehensive characterization of post-translational and chemical modifications of protein samples. However, not all mass shifts detected using the open search strategy represent true modifications, as artifacts exist from sources such as unaccounted missed cleavages or peptide co-fragmentation (chimeric MS/MS spectra). Here, we present Crystal-C, a computational tool that detects and removes such artifacts from open search results. Our analysis using Crystal-C shows that, in a typical shotgun proteomics data set, the number of such observations is relatively small. Nevertheless, removing these artifacts helps to simplify the interpretation of the mass shift histograms, which in turn should improve the ability of open search-based tools to detect potentially interesting mass shifts for follow-up investigation.
KW - LC-MS
KW - liquid chromatography coupled to mass spectrometry
KW - open search
KW - peptide identification
KW - post-translational modifications
UR - http://www.scopus.com/inward/record.url?scp=85086482005&partnerID=8YFLogxK
U2 - 10.1021/acs.jproteome.0c00119
DO - 10.1021/acs.jproteome.0c00119
M3 - 期刊論文
C2 - 32338005
AN - SCOPUS:85086482005
SN - 1535-3893
VL - 19
SP - 2511
EP - 2515
JO - Journal of Proteome Research
JF - Journal of Proteome Research
IS - 6
ER -