Search Databases and Statistics: Pitfalls and Best Practices in Phosphoproteomics

TY - CHAP

T1 - Search Databases and Statistics

T2 - Pitfalls and Best Practices in Phosphoproteomics

AU - Refsgaard, Jan C

AU - Munk, Stephanie

AU - Jensen, Lars J

PY - 2016/1/1

Y1 - 2016/1/1

N2 - Advances in mass spectrometric instrumentation in the past 15 years have resulted in an explosion in the raw data yield from typical phosphoproteomics workflows. This poses the challenge of confidently identifying peptide sequences, localizing phosphosites to proteins and quantifying these from the vast amounts of raw data. This task is tackled by computational tools implementing algorithms that match the experimental data to databases, providing the user with lists for downstream analysis. Several platforms for such automated interpretation of mass spectrometric data have been developed, each having strengths and weaknesses that must be considered for the individual needs. These are reviewed in this chapter. Equally critical for generating highly confident output datasets is the application of sound statistical criteria to limit the inclusion of incorrect peptide identifications from database searches. Additionally, careful filtering and use of appropriate statistical tests on the output datasets affects the quality of all downstream analyses and interpretation of the data. Our considerations and general practices on these aspects of phosphoproteomics data processing are presented here.

AB - Advances in mass spectrometric instrumentation in the past 15 years have resulted in an explosion in the raw data yield from typical phosphoproteomics workflows. This poses the challenge of confidently identifying peptide sequences, localizing phosphosites to proteins and quantifying these from the vast amounts of raw data. This task is tackled by computational tools implementing algorithms that match the experimental data to databases, providing the user with lists for downstream analysis. Several platforms for such automated interpretation of mass spectrometric data have been developed, each having strengths and weaknesses that must be considered for the individual needs. These are reviewed in this chapter. Equally critical for generating highly confident output datasets is the application of sound statistical criteria to limit the inclusion of incorrect peptide identifications from database searches. Additionally, careful filtering and use of appropriate statistical tests on the output datasets affects the quality of all downstream analyses and interpretation of the data. Our considerations and general practices on these aspects of phosphoproteomics data processing are presented here.

U2 - 10.1007/978-1-4939-3049-4_22

DO - 10.1007/978-1-4939-3049-4_22

M3 - Book chapter

C2 - 26584936

SN - 978-1-4939-3048-7

VL - 1355

T3 - Methods in molecular biology (Clifton, N.J.)

SP - 323

EP - 339

BT - Phospho-Proteomics

A2 - Stechow, Louise von

PB - Springer Publishing Company

ER -