ProteoCat: a tool for planning of proteomic experiments

Skvortsov, V. S.; Alekseychuk, N N; Khudyakov, D. V.; Mikurova, A V; Rybina, A. V.; Novikova, Svetlana; Tikhonova, Olga V.

doi:10.18097/pbmc20156106770

Cited by 4 publications

(2 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Gamma Анализ идентификации и степени покрытия последовательности предсказанными процедурами de novo пептидами выполняли при помощи программы ProteoCat [12], которая выполняет "побуквенное сравнение аминокислотной последовательности" белков и пептидов, при этом остатки изолейцинов и лейцинов считались эквивалентными, допускалась 1 аминокислотная замена. Обычно последнее допущение служит для поиска SAP, однако, в настоящей работе все подобные замены могли быть объяснены спонтанными модификациями при пробоподготовке или особенностями работы алгоритмов программ de novo секвенирования.…”

Section: O76070unclassified

Use of de novo sequencing for proteins identification

2017

Self Cite

View full text Add to dashboard Cite

Three de novo sequencing programs (Novor, PEAKS and PepNovo+) have been used for identification of 48 individual human proteins constituting the Universal Proteomics Standard Set 2 (UPS2) ("Sigma-Aldrich", USA). Experimental data have been obtained by tandem mass spectrometry. The MS/MS was performed using pure UPS2 and UPS2 mixtures with E. coli extract and human plasma samples. Protein detection was based on identification of at least two peptides of 9 residues in length or one peptide containing at least 13 residues. Using these criteria 13 (Novor), 20 (PEAKS) and 11 (PepNovo+) proteins were detected in pure UPS2 sample. Protein identifications in mixed samples were comparable or worse. Better results (by ~20%) were obtained using prediction included high quality identified fragment (TAG) containing at least 7 residues and unidentified additional masses at N- and C-termini (PepNovo+). The latter approach confidently recognized mass-spectrometric artefacts (and probably PTM). Atypical mass changes missed in UNIMOD DB were found (PepNovo+) to be statistically significant at the C-terminus (+23.02, +26.04 and +27.03). Using peptides containing these modifications and milder detection threshold 41 of 48 UPS2 proteins were identified.

show abstract

Section: O76070unclassified

Use of de novo sequencing for proteins identification

2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Анализ идентификации и степени покрытия последовательности предсказанными или найденными пептидами выполняли при помощи программы ProteoCat [13]. Использовали 2 варианта расчёта покрытия.…”

Section: анализ масс-спектрометрических данныхunclassified

The sequence coverage in different methods of mass spectrometry data analysis obtained on model proteins

et al. 2017

Self Cite

View full text Add to dashboard Cite

The aim of this study was to evaluate sequence coverage of five model proteins (CYB5A, SMAD4, RAB27B, FECH, and CXXC1) by means of shotgun proteomic data analysis employing different methods of data treatment including database-dependent search engines (MASCOT and X!Tandem) and de novo sequencing software ((PEAKS, Novor, and PepNovo+). In order to achieve maximal results, multiprotease hydrolysis including enzymes trypsin, LYS-C, ASPN and GluC was performed in solution and using the FASP method. High resolution mass spectrometry was carried out with a Q EXACTIVE HF hybrid mass spectrometer in the positive ionization mode; parent ions with the highest intensity and a charge range from +2 to +6 were fragmented in the HCD mode. 27 experiments were carried out (hydrolysis with each of 5 enzymes in solution, 4 for the FASP protocol, three technical repeats). Using parameters limiting false identification of peptides, the search engines and de novo sequencing software gave similar results. The degree of sequence coverage was not at least 40%, and in the best cases it reached 80-90%. The use of de novo sequencing software resulted in identification of the Y12H amino acid substitution in one model protein (CYB5A).

show abstract