Abstract
Mass spectrometry is extremely efficient for sequencing small peptides generated by, for example, a trypsin digestion of a complex mixture. Current instruments have the capacity to generate 50-100 K MSMS spectra from a single run. Of these ~30-50% is typically assigned to peptide matches on a 1% FDR threshold. The remaining spectra need more research to explain. We address here whether the 30-50% matched spectra provide consensus matches when using different database-dependent search pipelines. Although the majority of the spectra peptide assignments concur across search engines, our conclusion is that database-dependent search engines still require improvements.
| Original language | English |
|---|---|
| Pages (from-to) | 133-143 |
| Number of pages | 11 |
| Journal | Methods In Molecular Biology (Clifton, N.J.) |
| Volume | 2051 |
| DOIs | |
| Publication status | Published - 1 Jan 2020 |
Fingerprint
Keywords
- Database dependent search
- Peptide assignments
Cite this
}
Comparing Peptide Spectra Matches Across Search Engines. / Matthiesen, Rune; Prieto, Gorka; Beck, Hans Christian.
In: Methods In Molecular Biology (Clifton, N.J.), Vol. 2051, 01.01.2020, p. 133-143.Research output: Contribution to journal › Article
TY - JOUR
T1 - Comparing Peptide Spectra Matches Across Search Engines
AU - Matthiesen, Rune
AU - Prieto, Gorka
AU - Beck, Hans Christian
PY - 2020/1/1
Y1 - 2020/1/1
N2 - Mass spectrometry is extremely efficient for sequencing small peptides generated by, for example, a trypsin digestion of a complex mixture. Current instruments have the capacity to generate 50-100 K MSMS spectra from a single run. Of these ~30-50% is typically assigned to peptide matches on a 1% FDR threshold. The remaining spectra need more research to explain. We address here whether the 30-50% matched spectra provide consensus matches when using different database-dependent search pipelines. Although the majority of the spectra peptide assignments concur across search engines, our conclusion is that database-dependent search engines still require improvements.
AB - Mass spectrometry is extremely efficient for sequencing small peptides generated by, for example, a trypsin digestion of a complex mixture. Current instruments have the capacity to generate 50-100 K MSMS spectra from a single run. Of these ~30-50% is typically assigned to peptide matches on a 1% FDR threshold. The remaining spectra need more research to explain. We address here whether the 30-50% matched spectra provide consensus matches when using different database-dependent search pipelines. Although the majority of the spectra peptide assignments concur across search engines, our conclusion is that database-dependent search engines still require improvements.
KW - Database dependent search
KW - Peptide assignments
UR - http://www.scopus.com/inward/record.url?scp=85072623573&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-9744-2_5
DO - 10.1007/978-1-4939-9744-2_5
M3 - Article
VL - 2051
SP - 133
EP - 143
JO - Methods In Molecular Biology (Clifton, N.J.)
JF - Methods In Molecular Biology (Clifton, N.J.)
SN - 1064-3745
ER -