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@@ -58,3 +58,25 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
 human_hair_selected_with_GVPs_passed.mgf filter=lfs diff=lfs merge=lfs -text
+extracted/cptac2_human_hcd_itraq_phospho_selected.msp filter=lfs diff=lfs merge=lfs -text
+extracted/cptac2_human_hcd_itraq_selected_part1.msp filter=lfs diff=lfs merge=lfs -text
+extracted/cptac2_human_hcd_itraq_selected_part2.msp filter=lfs diff=lfs merge=lfs -text
+extracted/cptac3_tmt_selected_passed_best.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_consensus_final_true_lib.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_hair_selected_with_GVPs_passed.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_hcd_labelfree_phospho_selected_passed.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_hcd_semitryp.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_hcd_tryp_best.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_hcd_tryp_good.msp filter=lfs diff=lfs merge=lfs -text
+extracted/human_synthetic_hcd_selected.msp filter=lfs diff=lfs merge=lfs -text
+mgf/cptac2_human_hcd_itraq_phospho_selected.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/cptac2_human_hcd_itraq_selected_part1.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/cptac2_human_hcd_itraq_selected_part2.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/cptac3_tmt_selected_passed_best.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_consensus_final_true_lib.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_hair_selected_with_GVPs_passed.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_hcd_labelfree_phospho_selected_passed.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_hcd_semitryp.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_hcd_tryp_best.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_hcd_tryp_good.mgf filter=lfs diff=lfs merge=lfs -text
+mgf/human_synthetic_hcd_selected.mgf filter=lfs diff=lfs merge=lfs -text

download_list.txt

@@ -0,0 +1,11 @@
+https://chemdata.nist.gov/download/peptide_library/libraries/human/ION_TRAP/2014_05_29/2014_05_29_human_consensus_final_true_lib.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_best.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_tryp_good.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2020_05_19/human_hcd_semitryp.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_selected_part1.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_selected_part2.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/cptaclib/2015/cptac2_human_hcd_itraq_phospho_selected.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2017_05_30/human_synthetic_hcd_selected.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2019_02_14/human_hcd_labelfree_phospho_selected_passed.msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/hair/human_hair_selected_with_GVPs_passed_msp.tar.gz
+https://chemdata.nist.gov/download/peptide_library/libraries/human/HCD/2022_03_16/cptac3_tmt_selected_passed_best.msp.tar.gz

downloads/2014_05_29_human_consensus_final_true_lib.tar.gz

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msp_to_mgf.py

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+# -*- coding: utf-8 -*-
+import re
+from pathlib import Path
+from openpyxl import Workbook
+
+# =========================================================
+# 1) 路径配置：改这里即可
+#    INPUT_DIR : 你截图里的 extracted 目录（存放 .msp）
+#    OUTPUT_DIR: 输出 .mgf 的目录（会自动创建）
+#    EXCEL_PATH: 输出统计表
+# =========================================================
+INPUT_DIR = Path("/Users/guanmumu/Desktop/Data/Human/extracted")
+OUTPUT_DIR = Path("/Users/guanmumu/Desktop/Data/Human/mgf")
+OUTPUT_DIR.mkdir(parents=True, exist_ok=True)
+
+EXCEL_PATH = OUTPUT_DIR / "msp_to_mgf_summary.xlsx"
+
+# 进度打印（大文件可调）
+PROGRESS_EVERY_SPECTRA = 50000
+
+# =========================================================
+# 2) MSP 字段解析函数（保持和你单文件脚本一致）
+# =========================================================
+def parse_sequence_from_name(name_val: str) -> str:
+    # Name: SEQUENCE/charge_...
+    return name_val.split("/", 1)[0].strip()
+
+def parse_charge_from_name(name_val: str):
+    m = re.search(r"/(\d+)", name_val)
+    return int(m.group(1)) if m else None
+
+def parse_mz_exact_from_comment(line: str):
+    # Comment: ... Mz_exact=536.5844 ...
+    m = re.search(r"\bMz_exact=([0-9]*\.?[0-9]+)", line)
+    return float(m.group(1)) if m else None
+
+# =========================================================
+# 3) 转换单个 MSP -> MGF，并返回统计信息
+#    - Spectra count: Num peaks 次数
+#    - Unique peptides: 对 Name: 的 seq 去重（与你单文件脚本一致）
+# =========================================================
+def convert_one_msp(msp_path: Path, mgf_path: Path):
+    spectra_count = 0
+    unique_peptides = set()
+
+    with msp_path.open("r", encoding="utf-8", errors="replace") as fin, \
+         mgf_path.open("w", encoding="utf-8") as fout:
+
+        name_val = None
+        seq = None
+        charge = None
+        mw = None               # 你要求用作 PEPMASS
+        precursor_mz = None     # 仅用于辅助记录（Mz_exact）
+
+        for line in fin:
+            line = line.rstrip("\n")
+
+            if line.startswith("Name:"):
+                name_val = line.split("Name:", 1)[1].strip()
+                seq = parse_sequence_from_name(name_val)
+                charge = parse_charge_from_name(name_val)
+                unique_peptides.add(seq)
+
+            elif line.startswith("MW:"):
+                try:
+                    mw = float(line.split("MW:", 1)[1].strip())
+                except Exception:
+                    mw = None
+
+            elif line.startswith("Comment:"):
+                precursor_mz = parse_mz_exact_from_comment(line)
+
+            elif line.startswith("Num peaks:"):
+                num_peaks = int(line.split("Num peaks:", 1)[1].strip())
+                spectra_count += 1
+
+                # ===== 写一个 MGF block =====
+                fout.write("BEGIN IONS\n")
+
+                if seq is not None and charge is not None:
+                    fout.write(f"TITLE={seq}/z{charge}\n")
+                elif seq is not None:
+                    fout.write(f"TITLE={seq}\n")
+                else:
+                    fout.write(f"TITLE=Spectrum_{spectra_count}\n")
+
+                # 你要求：PEPMASS = MW（不做换算）
+                if mw is not None:
+                    fout.write(f"PEPMASS={mw:.6f}\n")
+
+                if charge is not None:
+                    fout.write(f"CHARGE={charge}+\n")
+
+                # 自定义字段
+                if seq is not None:
+                    fout.write(f"SEQ={seq}\n")
+
+                # 可选：记录 Mz_exact（不影响你要求）
+                if precursor_mz is not None:
+                    fout.write(f"PRECURSOR_MZ={precursor_mz:.6f}\n")
+
+                # 峰：每行 "m/z intensity"
+                for _ in range(num_peaks):
+                    peak_line = next(fin).strip()
+                    if not peak_line:
+                        continue
+                    parts = peak_line.split()
+                    if len(parts) >= 2:
+                        fout.write(f"{parts[0]} {parts[1]}\n")
+
+                fout.write("END IONS\n\n")
+
+                # reset 当前谱状态（与你单文件脚本一致）
+                name_val = None
+                seq = None
+                charge = None
+                mw = None
+                precursor_mz = None
+
+                if spectra_count % PROGRESS_EVERY_SPECTRA == 0:
+                    print(f"  ... {msp_path.name}: spectra={spectra_count}")
+
+    return spectra_count, len(unique_peptides)
+
+# =========================================================
+# 4) 写 Excel（3列：文件名 / Spectra count / Unique peptides）
+# =========================================================
+def write_excel(excel_path: Path, rows):
+    wb = Workbook()
+    ws = wb.active
+    ws.title = "summary"
+
+    for r in rows:
+        ws.append(list(r))
+
+    ws.column_dimensions["A"].width = 55
+    ws.column_dimensions["B"].width = 18
+    ws.column_dimensions["C"].width = 20
+
+    wb.save(excel_path)
+
+# =========================================================
+# 5) 批量处理
+# =========================================================
+def main():
+    if not INPUT_DIR.exists():
+        raise FileNotFoundError(f"INPUT_DIR not found: {INPUT_DIR}")
+
+    msp_files = sorted(INPUT_DIR.glob("*.msp"))
+    if not msp_files:
+        print(f"No .msp files found in: {INPUT_DIR}")
+        return
+
+    print(f"Input dir : {INPUT_DIR}")
+    print(f"Output dir: {OUTPUT_DIR}")
+    print(f"Found {len(msp_files)} MSP files.")
+
+    rows = [("file_name", "spectra_count", "unique_peptides")]
+
+    for idx, msp_path in enumerate(msp_files, 1):
+        mgf_path = OUTPUT_DIR / (msp_path.stem + ".mgf")
+
+        print(f"\n[{idx}/{len(msp_files)}] Converting: {msp_path.name}")
+        spectra_count, unique_pep = convert_one_msp(msp_path, mgf_path)
+
+        print(f"  -> MGF: {mgf_path.name}")
+        print(f"  Spectra count   : {spectra_count}")
+        print(f"  Unique peptides : {unique_pep}")
+
+        rows.append((msp_path.name, spectra_count, unique_pep))
+
+    write_excel(EXCEL_PATH, rows)
+
+    print("\n================= DONE =================")
+    print(f"Excel summary: {EXCEL_PATH}")
+
+if __name__ == "__main__":
+    main()

msp_to_mgf_副本.py

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+# -*- coding: utf-8 -*-
+import os
+import re
+
+# =========================================================
+# 1) 读取路径与保存路径（请你按自己的电脑路径修改）
+# =========================================================
+# 示例（macOS）:
+MSP_PATH = "/Users/guanmumu/Desktop/Data/Human/extracted/human_hair_selected_with_GVPs_passed.msp"
+MGF_PATH = "/Users/guanmumu/Desktop/Data/human_hair_selected_with_GVPs_passed.mgf"
+
+# 如果你想让脚本“放哪儿都能跑”，可以用脚本所在目录：
+# BASE_DIR = os.path.dirname(os.path.abspath(__file__))
+# MSP_PATH = os.path.join(BASE_DIR, "bsa_consensus_final_true_lib.msp")
+# MGF_PATH = os.path.join(BASE_DIR, "bsa_consensus_final_true_lib.pepmass_is_mw.mgf")
+
+# =========================================================
+# 2) MSP 字段解析函数
+# =========================================================
+def parse_sequence_from_name(name_val: str) -> str:
+    # Name: SEQUENCE/charge_...
+    return name_val.split("/")[0].strip()
+
+def parse_charge_from_name(name_val: str):
+    m = re.search(r"/(\d+)", name_val)
+    return int(m.group(1)) if m else None
+
+def parse_mz_exact_from_comment(line: str):
+    # Comment: ... Mz_exact=536.5844 ...
+    m = re.search(r"\bMz_exact=([0-9]*\.?[0-9]+)", line)
+    return float(m.group(1)) if m else None
+
+# =========================================================
+# 3) 主逻辑：流式读取 MSP，写 MGF
+# =========================================================
+def main():
+    spectra_count = 0
+    unique_peptides = set()
+
+    with open(MSP_PATH, "r", encoding="utf-8", errors="replace") as fin, \
+         open(MGF_PATH, "w", encoding="utf-8") as fout:
+
+        name_val = None
+        seq = None
+        charge = None
+        mw = None               # 你要求用作 PEPMASS
+        precursor_mz = None     # 仅用于辅助记录（Mz_exact）
+
+        for line in fin:
+            line = line.rstrip("\n")
+
+            if line.startswith("Name:"):
+                name_val = line.split("Name:", 1)[1].strip()
+                seq = parse_sequence_from_name(name_val)
+                charge = parse_charge_from_name(name_val)
+                unique_peptides.add(seq)
+
+            elif line.startswith("MW:"):
+                try:
+                    mw = float(line.split("MW:", 1)[1].strip())
+                except Exception:
+                    mw = None
+
+            elif line.startswith("Comment:"):
+                precursor_mz = parse_mz_exact_from_comment(line)
+
+            elif line.startswith("Num peaks:"):
+                # 进入峰列表块
+                num_peaks = int(line.split("Num peaks:", 1)[1].strip())
+
+                spectra_count += 1
+
+                # ===================== 写一个 MGF block =====================
+                fout.write("BEGIN IONS\n")
+
+                # TITLE：建议写得可追溯
+                if seq is not None and charge is not None:
+                    fout.write(f"TITLE={seq}/z{charge}\n")
+                elif seq is not None:
+                    fout.write(f"TITLE={seq}\n")
+                else:
+                    fout.write(f"TITLE=Spectrum_{spectra_count}\n")
+
+                # 你要求：PEPMASS = MW（不做换算）
+                # 注意：如果 mw 缺失，会跳过 PEPMASS 行
+                if mw is not None:
+                    fout.write(f"PEPMASS={mw:.6f}\n")
+
+                # 电荷
+                if charge is not None:
+                    fout.write(f"CHARGE={charge}+\n")
+
+                # 你要的 sequence 列：这里写在 MGF 自定义字段中
+                if seq is not None:
+                    fout.write(f"SEQ={seq}\n")
+
+                # 辅助字段：把 Comment 里 Mz_exact 也记录下来（不影响你要求）
+                if precursor_mz is not None:
+                    fout.write(f"PRECURSOR_MZ={precursor_mz:.6f}\n")
+
+                # 写峰：每行 "m/z intensity"
+                for _ in range(num_peaks):
+                    peak_line = next(fin).strip()
+                    if not peak_line:
+                        continue
+                    parts = peak_line.split()
+                    if len(parts) >= 2:
+                        mz = parts[0]
+                        inten = parts[1]
+                        fout.write(f"{mz} {inten}\n")
+
+                fout.write("END IONS\n\n")
+
+                # reset 当前谱状态
+                name_val = None
+                seq = None
+                charge = None
+                mw = None
+                precursor_mz = None
+
+    # =========================================================
+    # 4) 最终统计输出
+    # =========================================================
+    print(f"[DONE] MSP input : {MSP_PATH}")
+    print(f"[DONE] MGF output: {MGF_PATH}")
+    print(f"Spectra count      : {spectra_count}")
+    print(f"Unique peptides    : {len(unique_peptides)}")
+
+if __name__ == "__main__":
+    main()