Progressive Search

• Performance

The entire experiments were carried out on a Linux PC with an Intel(R) Xeon(R) CPU E5-2609 v3 @ 1.90GHz and 36GB of RAM. The Linux version is Ubuntu 12.04.5 LTS and the compiler is GNU C compiler 6.5.0.

(A) Search time comparison between the normal search from scratch and the progressive search, both of which are implemented on Comet. Comparisons were done in different settings of number of tryptic termini (ntt) and missed cleavages (mc) where the difference between the old DB and the new DB is 0.2%. In general, the more nontryptic termini and missed cleavages there are, the faster the progressive search is: For ntt2mc0, it is 17.1 times faster for PSM update only and 4.1 times faster for both PSM and E-value update. For ntt1mc2, it is 53.9 times faster for PSM update only and 16.5 times faster for both PSM and E-value update.

(B) Search time comparison according to database update intervals for ntt1mc2. For this analysis, the Uniprot databases from January to June 2020 are used. The difference between the old DB and the new DB is 0.2% for 1 month, 2.0 % for 2 months, 2.4% for 3 months, 2.6% for 4 months and 3.9% for 5 months, respectively. The speed-up decreases as the difference increases: from 53.9 for 1 month to 17.4 for 5 months for PSM update only and from 16.5 for 1 month to 10.2 for 5 months for both PSM and E-value update.

• Software

Download

Download ProgressiveSearch.jar and SampleData.zip in the same directory and unzip SampleData.zip.

ProgressiveSearch     ProgressiveSearch.jar    (64-bit Linux on x86 CPU)

Sample data               SampleData.zip

Source code               ProgressiveSearch(Source).zip

                                        Comet-E(Source).zip
                                        Comet-P(Source).zip

Usage

1. Comet-P
java -jar ProgressiveSearch.jar  Comet-P  <oldDB_result>  <oldDB>  <newDB>  <Spectrum>  <Comet_param>  <out_dir>

( Use this command for the sample data: java -jar ProgressiveSearch.jar Comet-P oldDB_result.txt uniprot_2020_01_withDecoy.fasta uniprot_2020_02_withDecoy.fasta sample.mgf comet.params output_Comet-P )

2. Comet-E
java -jar ProgressiveSearch.jar  Comet-E  <oldDB_result>  <oldDB_result_histogram>  <oldDB>  <newDB>  <Spectrum>  <Comet_param>  <out_dir>

( Use this command for the sample data: java -jar ProgressiveSearch.jar Comet-E oldDB_result.txt oldDB_result_histogram.txt uniprot_2020_01_withDecoy.fasta uniprot_2020_02_withDecoy.fasta sample.mgf comet.params output_Comet-E )

Parameter descriptions

<oldDB_result>:  Comet result of the old DB

<oldDB_result_histogram>:  Comet histogram of old DB result

<oldDB>:  old DB (.fasta)

<newDB>:  new DB (.fasta)

<Spectrum>:  spectrum set (.mgf)

<Comet_param>:  Comet parameters (.params)

<out_dir>:  output directory

Output files in <out_dir>

Comet-P_result.txt:  result of Comet-P

Comet-E_result.txt:  result of Comet-E (Comet-E only)

deleted.fasta:  deleted DB

shared.fasta:  shared DB

inserted.fasta:  inserted DB

deletion_result.txt:  Comet result of the shared DB for extracted spectra

deletedDB_result.txt:  Comet result of the deleted DB (Comet-E only)

insertedDB_result.txt:  Comet result of the inserted DB

<Spectrum>_extracted.mgf:  spectrum set for deletion

deletion_result_histogram.txt:  Comet histogram of shared DB result for extracted spectra (Comet-E only)

deletedDB_result_histogram.txt:  Comet histogram of deleted DB result (Comet-E only)

insertedDB_result_histogram.txt:  Comet histogram of inserted DB result (Comet-E only)

newDB_result_histogram.txt:  Comet histogram of new DB result (Comet-E only)

For Comet_Param options in detail, refer to https://uwpr.github.io/Comet/parameters/.