An Automated Method for Scanning LC−MS Data Sets for Significant Peptides and Proteins, Including Quantitative Profiling and Interactive Confirmation: An Automated Method for Scanning LC−MS Data Sets for Significant Peptides and Proteins, Including Quantitative Profiling and Interactive Confirmation

An Automated Method for Scanning LC−MS Data Sets for Significant Peptides and Proteins, Including Quantitative Profiling and Interactive Confirmation : An Automated Method for Scanning LC−MS Data Sets for Significant Peptides and Proteins, Including Quantitative Profiling and Interactive Confirmation

Differential quantification of proteins and peptides by LC-MS is a promising method to acquire knowledge about biological processes, and for finding drug targets and biomarkers. However, differential protein analysis using LC-MS has been held back by the lack of suitable software tools. Large amounts of experimental data are easily generated in protein and peptide profiling experiments, but data analysis is time-consuming and labor-intensive. Here, we present a fully automated method for scanning LC-MS/MS data for biologically significant peptides and proteins, including support for interactive confirmation and further profiling. By studying peptide mixtures of known composition, we demonstrate that peptides present in different amounts in different groups of samples can be automatically screened for using statistical tests. A linear response can be obtained over almost 3 orders of magnitude, facilitating further profiling of peptides and proteins of interest. Furthermore, we apply the method to study the changes of endogenous peptide levels in mouse brain striatum after administration of reserpine, a classical model drug for inducing Parkinson disease symptoms.

Söderström, Malin (författare)
Fenyö, David (författare)
Nilsson, AnnaUppsala universitet,MMS, medicinsk masspektrometri (författare)
Fälth, MariaUppsala universitet,MMS, medicinsk masspektrometri (författare)
Sköld, KarlUppsala universitet,MMS, medicinsk masspektrometri (författare)
Svensson, MarcusUppsala universitet,MMS, medicinsk masspektrometri (författare)
Pettersen, Harald (författare)
Lindqvist, Staffan (författare)
Svenningsson, Per (författare)
Andrén, Per E.Uppsala universitet,MMS, medicinsk masspektrometri(Swepub:uu)perandre (författare)
Björkesten, Lennart (författare)
Uppsala universitetMMS, medicinsk masspektrometri (creator_code:org_t)

Ingår i:Journal of Proteome Research: American Chemical Society (ACS)6:7, s. 2888-28951535-38931535-3907

Av författaren/redakt...: Kaplan, Anders; Söderström, Mali ...; Fenyö, David; Nilsson, Anna; Fälth, Maria; Sköld, Karl; visa fler...; Svensson, Marcus; Pettersen, Haral ...; Lindqvist, Staff ...; Svenningsson, Pe ...; Andrén, Per E.; Björkesten, Lenn ...; visa färre...

Om ämnet

MEDICIN OCH HÄLSOVETENSKAP: MEDICIN OCH HÄLS ...; och Medicinska och f ...; och Farmaceutiska ve ...

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.