diff --git a/inst/tinytest/raw_data/DIANN/PXD055942.parquet b/inst/tinytest/raw_data/DIANN/PXD055942.parquet index c576365a..28076bc6 100644 Binary files a/inst/tinytest/raw_data/DIANN/PXD055942.parquet and b/inst/tinytest/raw_data/DIANN/PXD055942.parquet differ diff --git a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R index afc81743..b03d286d 100644 --- a/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R +++ b/inst/tinytest/test_converters_DIANNtoMSstatsFormat.R @@ -120,7 +120,7 @@ output_pxd_dt = data.table::as.data.table(output_pxd) # Basic structure expect_equal(ncol(output_pxd), 11) -expect_equal(nrow(output_pxd), 20400) +expect_equal(nrow(output_pxd), 23568) expect_true("Run" %in% colnames(output_pxd)) expect_true("ProteinName" %in% colnames(output_pxd)) expect_true("PeptideSequence" %in% colnames(output_pxd)) @@ -136,17 +136,17 @@ expect_true("Fraction" %in% colnames(output_pxd)) # Channel path used: H/L/NA counts, no "Light" default expect_false("Light" %in% output_pxd$IsotopeLabelType) pxd_label_counts = table(output_pxd$IsotopeLabelType, useNA = "ifany") -expect_equal(unname(pxd_label_counts["H"]), 8712L) -expect_equal(unname(pxd_label_counts["L"]), 8712L) -expect_equal(sum(is.na(output_pxd$IsotopeLabelType)), 2976L) +expect_equal(unname(pxd_label_counts["H"]), 9720L) +expect_equal(unname(pxd_label_counts["L"]), 9720L) +expect_equal(sum(is.na(output_pxd$IsotopeLabelType)), 4128L) # Channel path does NOT strip (SILAC) from PeptideSequence — that notation is # part of the peptide identity in this format, not a label indicator expect_true(any(grepl("(SILAC)", output_pxd$PeptideSequence, fixed = TRUE))) # Unlabeled peptides (no K, no SILAC) get NA IsotopeLabelType -pxd_unlabeled = output_pxd_dt[PeptideSequence %in% c("AVLEEAEFQR", "DDEGLYTLR", - "DTELAEELLQWFLQEEK")] +pxd_unlabeled = output_pxd_dt[PeptideSequence %in% c("AAATFNPELITHILDGSPENTR", "AAASLDTAALSATDMALALNR", + "AIMHHEGHMDDGLNLSR")] expect_true(all(is.na(pxd_unlabeled$IsotopeLabelType))) # Annotation maps correctly to all three timepoint conditions @@ -156,27 +156,19 @@ expect_true("32 days" %in% output_pxd$Condition) run_0d = "20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_0d_1" expect_equal(as.character(unique(output_pxd_dt[Run == run_0d, Condition])), "0 day") -# Heavy fragment intensities match Fr.N.Quantity from the Channel = "H" input row. -# Input: AFMTADLPNELIELLEK(SILAC)(SILAC)(SILAC), Run 32d_1, Channel H has -# Fr.0.Quantity = 662450.1 (largest fragment — should be the max output intensity) -h_pxd_pep = "AFMTADLPNELIELLEK(SILAC)(SILAC)(SILAC)" +h_pxd_pep = "TAFDDAIAELDTLNEDSYK(SILAC)(SILAC)(SILAC)" h_pxd_run = "20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_32d_1" h_pxd_ints = output_pxd_dt[PeptideSequence == h_pxd_pep & IsotopeLabelType == "H" & Run == h_pxd_run, Intensity] -expect_equal(max(h_pxd_ints, na.rm = TRUE), 662450.1, tolerance = 1) +expect_equal(max(h_pxd_ints, na.rm = TRUE), 2453057.5, tolerance = 1) -# Light fragment intensities match Fr.N.Quantity from the Channel = "L" input row. -# Input: APVYSGSSPVSGYFVDFK(SILAC)(SILAC)(SILAC)EEDSGEWK(SILAC)(SILAC)(SILAC), -# Run 32d_2, Channel L has Fr.1.Quantity = 116961.9 (largest fragment) -l_pxd_pep = "APVYSGSSPVSGYFVDFK(SILAC)(SILAC)(SILAC)EEDSGEWK(SILAC)(SILAC)(SILAC)" -l_pxd_run = "20210805_BoxCarmax1st_wideMS1_JM_pSIL_pro_heart_32d_2" +l_pxd_pep = "TAFDDAIAELDTLNEDSYK(SILAC)(SILAC)(SILAC)" +l_pxd_run = "20210805_BoxCarmax2nd_wideMS1_JM_pSIL_pro_heart_0d_1" l_pxd_ints = output_pxd_dt[PeptideSequence == l_pxd_pep & IsotopeLabelType == "L" & Run == l_pxd_run, Intensity] -expect_equal(max(l_pxd_ints, na.rm = TRUE), 116961.9, tolerance = 1) -# Fr.0.Quantity = 4973.411 also appears in the output -expect_true(any(abs(l_pxd_ints - 4973.411) < 1, na.rm = TRUE)) +expect_equal(max(l_pxd_ints, na.rm = TRUE), 4686039.5, tolerance = 1) # Test DIANNtoMSstatsFormat --------------------------- input_file_path = system.file("tinytest/raw_data/DIANN/diann_input.tsv", package="MSstatsConvert")